##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IFAA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IFAA_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/IFAA.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IFAA/DESCRIPTION’ ... OK
* this is package ‘IFAA’ version ‘1.4.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IFAA’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
IFAA  22.523  0.312 120.120
MZILN  1.698  0.041  25.897
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IFAA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘IFAA’ ...
** 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 (IFAA)

R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.

> BiocGenerics:::testPackage("IFAA")
Data dimensions (after removing missing data if any):
40 samples
20 taxa/OTU/ASV
2 testCov variables in the analysis
These are the testCov variables:
x1, x2
1 ctrlCov variables in the analysis 
These are the ctrlCov variables:
x3
1 binary covariates in the analysis
These are the binary covariates:
x2 
25 percent of microbiome sequencing reads are zero
Start Phase 1 analysis
2 parallel jobs are registered for the analysis.
33 percent of phase 1 analysis has been done and it took 0.32 minutes
2 parallel jobs are registered for the analysis.
100 percent of phase 1 analysis has been done and it took 0.6 minutes
Start Phase 2 parameter estimation
2 parallel jobs are registered for analyzing reference taxa in Phase 2
50 percent of Phase 2 is done and it took 0.218 minutes
2 parallel jobs are registered for analyzing reference taxa in Phase 2
Entire Phase 2 parameter estimation done and took 0.431 minutes.
The entire analysis took 1.04 minutes
Data dimensions (after removing missing data if any):
40 samples
20 taxa/OTU/ASV
3 testCov variables in the analysis
These are the testCov variables:
x1, x2, x3
0 ctrlCov variables in the analysis 
1 binary covariates in the analysis
These are the binary covariates:
x2 
25 percent of microbiome sequencing reads are zero
2 parallel jobs are registered for analyzing reference taxa in Phase 2
Estimation done for the 1th denominator taxon: rawCount10 and it took 0.21 minutes
The entire analysis took 0.21 minutes
Data dimensions (after removing missing data if any):
5 samples
20 taxa/OTU/ASV
2 testCov variables in the analysis
These are the testCov variables:
x1, x2
4 ctrlCov variables in the analysis 
These are the ctrlCov variables:
x3, x4, x5, x6
1 binary covariates in the analysis
These are the binary covariates:
x2 
0 percent of microbiome sequencing reads are zero
Start Phase 1 analysis
2 parallel jobs are registered for the analysis.
33 percent of phase 1 analysis has been done and it took 0.24 minutes
2 parallel jobs are registered for the analysis.
67 percent of phase 1 analysis has been done and it took 0.49 minutes
2 parallel jobs are registered for the analysis.
100 percent of phase 1 analysis has been done and it took 0.74 minutes
Start Phase 2 parameter estimation
2 parallel jobs are registered for analyzing reference taxa in Phase 2
50 percent of Phase 2 is done and it took 0.353 minutes
2 parallel jobs are registered for analyzing reference taxa in Phase 2
Entire Phase 2 parameter estimation done and took 0.744 minutes.
The entire analysis took 1.48 minutes


RUNIT TEST PROTOCOL -- Sun Mar  3 21:23:10 2024 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IFAA RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 37.380   0.922 174.154