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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:FinfoMDS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings FinfoMDS_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FinfoMDS.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘FinfoMDS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FinfoMDS’ 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 ... 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 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 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 15.034  0.178  15.214
* 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:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL FinfoMDS
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘FinfoMDS’ ...
** this is package ‘FinfoMDS’ version ‘1.0.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> # 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 23.20   mds 8.59   conf 29.23   p_z 0.127   p_0 0.178
epoch 1   lambda 0.5   total 134.78   mds 5.66   conf 258.24   p_z 0.695   p_0 0.178
epoch 2   lambda 0.5   total 43.83   mds 4.49   conf 78.69   p_z 0.280   p_0 0.178
epoch 3   lambda 0.5   total 78.94   mds 4.87   conf 148.13   p_z 0.069   p_0 0.178
epoch 4   lambda 0.5   total 142.33   mds 4.89   conf 274.88   p_z 0.695   p_0 0.178
epoch 5   lambda 0.5   total 48.55   mds 3.95   conf 89.22   p_z 0.289   p_0 0.178
epoch 6   lambda 0.5   total 71.67   mds 4.44   conf 134.46   p_z 0.061   p_0 0.178
epoch 7   lambda 0.5   total 139.08   mds 4.80   conf 268.58   p_z 0.701   p_0 0.178
epoch 8   lambda 0.5   total 37.38   mds 3.78   conf 67.20   p_z 0.265   p_0 0.178
epoch 9   lambda 0.5   total 100.17   mds 4.45   conf 191.45   p_z 0.046   p_0 0.178
epoch 10   lambda 0.5   total 136.36   mds 4.73   conf 263.25   p_z 0.642   p_0 0.178
epoch 11   lambda 0.5   total 19.20   mds 3.71   conf 31.00   p_z 0.239   p_0 0.178
epoch 12   lambda 0.5   total 123.71   mds 4.46   conf 238.48   p_z 0.044   p_0 0.178
epoch 13   lambda 0.5   total 132.97   mds 4.72   conf 256.50   p_z 0.680   p_0 0.178
epoch 14   lambda 0.5   total 33.95   mds 3.67   conf 60.56   p_z 0.238   p_0 0.178
epoch 15   lambda 0.5   total 131.77   mds 4.47   conf 254.60   p_z 0.022   p_0 0.178
epoch 16   lambda 0.5   total 108.29   mds 4.70   conf 207.19   p_z 0.647   p_0 0.178
epoch 17   lambda 0.5   total 28.14   mds 3.57   conf 49.13   p_z 0.196   p_0 0.178
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 21.64   mds 3.02   conf 37.24   p_z 0.041   p_0 0.057
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 21.64   mds 3.02   conf 37.24   p_z 0.041   p_0 0.057
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 
 64.800   0.655  65.449