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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 15.164  0.192  15.356
* 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 21.85   mds 2.96   conf 37.79   p_z 0.009   p_0 0.005
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 29.01   mds 2.06   conf 53.90   p_z 0.284   p_0 0.173
epoch 1   lambda 0.5   total 53.81   mds 1.66   conf 104.31   p_z 0.062   p_0 0.173
epoch 2   lambda 0.5   total 77.63   mds 1.79   conf 151.68   p_z 0.597   p_0 0.173
epoch 3   lambda 0.5   total 18.10   mds 1.40   conf 33.40   p_z 0.264   p_0 0.173
epoch 4   lambda 0.5   total 59.08   mds 1.71   conf 114.73   p_z 0.058   p_0 0.173
epoch 5   lambda 0.5   total 80.58   mds 1.76   conf 157.65   p_z 0.648   p_0 0.173
epoch 6   lambda 0.5   total 16.79   mds 1.38   conf 30.81   p_z 0.260   p_0 0.173
epoch 7   lambda 0.5   total 60.84   mds 1.70   conf 118.27   p_z 0.058   p_0 0.173
epoch 8   lambda 0.5   total 74.18   mds 1.73   conf 144.89   p_z 0.628   p_0 0.173
epoch 9   lambda 0.5   total 25.03   mds 1.36   conf 47.33   p_z 0.244   p_0 0.173
epoch 10   lambda 0.5   total 65.33   mds 1.71   conf 127.25   p_z 0.048   p_0 0.173
epoch 11   lambda 0.5   total 78.78   mds 1.72   conf 154.12   p_z 0.626   p_0 0.173
epoch 12   lambda 0.5   total 17.39   mds 1.37   conf 32.05   p_z 0.222   p_0 0.173
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 29.01   mds 2.06   conf 53.90   p_z 0.284   p_0 0.173
epoch 1   lambda 0.5   total 53.81   mds 1.66   conf 104.31   p_z 0.062   p_0 0.173
epoch 2   lambda 0.5   total 77.63   mds 1.79   conf 151.68   p_z 0.597   p_0 0.173
epoch 3   lambda 0.5   total 18.10   mds 1.40   conf 33.40   p_z 0.264   p_0 0.173
epoch 4   lambda 0.5   total 59.08   mds 1.71   conf 114.73   p_z 0.058   p_0 0.173
epoch 5   lambda 0.5   total 80.58   mds 1.76   conf 157.65   p_z 0.648   p_0 0.173
epoch 6   lambda 0.5   total 16.79   mds 1.38   conf 30.81   p_z 0.260   p_0 0.173
epoch 7   lambda 0.5   total 60.84   mds 1.70   conf 118.27   p_z 0.058   p_0 0.173
epoch 8   lambda 0.5   total 74.18   mds 1.73   conf 144.89   p_z 0.628   p_0 0.173
epoch 9   lambda 0.5   total 25.03   mds 1.36   conf 47.33   p_z 0.244   p_0 0.173
epoch 10   lambda 0.5   total 65.33   mds 1.71   conf 127.25   p_z 0.048   p_0 0.173
epoch 11   lambda 0.5   total 78.78   mds 1.72   conf 154.12   p_z 0.626   p_0 0.173
epoch 12   lambda 0.5   total 17.39   mds 1.37   conf 32.05   p_z 0.222   p_0 0.173
Lambda 0.50 ...halt iteration
epoch 0   lambda 0.5   total 10.34   mds 3.51   conf 13.66   p_z 0.031   p_0 0.031
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 
 75.106   0.676  75.774