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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCM_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/RCM.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘RCM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCM’ version ‘1.26.0’
* 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 ‘RCM’ 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
RCM_NB            68.006  1.711  71.332
permanova         22.561  0.276  23.655
addOrthProjection 16.870  0.457  17.418
plotRespFun       16.596  0.144  16.821
plot.RCM          16.135  0.270  17.284
RCM               15.264  0.440  15.760
inertia           14.836  0.273  17.265
liks              14.334  0.220  16.420
extractCoord      14.067  0.267  14.396
getDevianceRes    11.418  0.305  12.094
* 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:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RCM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RCM’ ...
** this is package ‘RCM’ version ‘1.26.0’
** using staged installation
** R
** data
** 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 (RCM)

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-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.

> library(testthat)
> library(RCM)
> library(phyloseq)
> data(Zeller)
> test_check("RCM")
Permutation 1 out of 10000 
Permutation 1001 out of 10000 
Permutation 2001 out of 10000 
Permutation 3001 out of 10000 
Permutation 4001 out of 10000 
Permutation 5001 out of 10000 
Permutation 6001 out of 10000 
Permutation 7001 out of 10000 
Permutation 8001 out of 10000 
Permutation 9001 out of 10000 
Permutation 1 out of 10000 
Permutation 1001 out of 10000 
Permutation 2001 out of 10000 
Permutation 3001 out of 10000 
Permutation 4001 out of 10000 
Permutation 5001 out of 10000 
Permutation 6001 out of 10000 
Permutation 7001 out of 10000 
Permutation 8001 out of 10000 
Permutation 9001 out of 10000 
Permutation 1 out of 20 
Permutation 3 out of 20 
Permutation 5 out of 20 
Permutation 7 out of 20 
Permutation 9 out of 20 
Permutation 11 out of 20 
Permutation 13 out of 20 
Permutation 15 out of 20 
Permutation 17 out of 20 
Permutation 19 out of 20 
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
169.999   5.682 177.383