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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FinfoMDS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FinfoMDS_0.99.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FinfoMDS.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FinfoMDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FinfoMDS’ version ‘0.99.2’
* 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 ‘FinfoMDS’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
fmds 17.507  0.261  17.885
* 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 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 FinfoMDS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘FinfoMDS’ ...
** this is package ‘FinfoMDS’ version ‘0.99.2’
** 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 (FinfoMDS)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(FinfoMDS)
> 
> test_check("FinfoMDS")
epoch 0   lambda 0.5   total 17.17   mds 5.54   conf 23.28   p_z 0.067   p_0 0.118
epoch 1   lambda 0.5   total 134.33   mds 5.70   conf 257.25   p_z 0.467   p_0 0.118
epoch 2   lambda 0.5   total 36.48   mds 3.94   conf 65.08   p_z 0.052   p_0 0.118
epoch 3   lambda 0.5   total 156.38   mds 5.60   conf 301.56   p_z 0.519   p_0 0.118
epoch 4   lambda 0.5   total 7.13   mds 3.98   conf 6.31   p_z 0.108   p_0 0.118
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 24.69   mds 6.92   conf 35.55   p_z 0.075   p_0 0.113
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 24.69   mds 6.92   conf 35.55   p_z 0.075   p_0 0.113
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 11.85   mds 3.58   conf 16.54   p_z 0.004   p_0 0.001
epoch 1   lambda 0.5   total 352.48   mds 5.18   conf 694.59   p_z 0.000   p_0 0.001
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 300.00   mds 0.00   conf 600.00   p_z 0.000   p_0 0.000
Lambda 0.50 ...halt iteration
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 41.896   0.797  42.969