##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ramr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ramr_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ramr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ramr/DESCRIPTION’ ... OK
* this is package ‘ramr’ version ‘1.8.0’
* 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 ‘ramr’ 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 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
ramr.data 17.458  0.926  18.694
getAMR    16.050  0.843  16.355
plotAMR    3.615  0.077   5.488
* 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 ramr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘ramr’ ...
** 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 (ramr)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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("ramr")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Identifying AMRsIdentifying AMRs [11.351s]
Identifying AMRs [14.777s]
Identifying AMRs [15.330s]
Identifying AMRs [6.562s]
'nsamples' has been set to the maximum possible value of 143
'regions.per.sample' has been set to the maximum possible value of 1
'samples.per.region' has been set to the maximum possible value of 143
'regions.per.sample' has been set to the maximum possible value of 4
'regions.per.sample' has been set to the maximum possible value of 15
Simulating data [1.941s]
Introducing epimutations [0.154s]
Simulating data [1.914s]
Introducing epimutations [0.174s]


RUNIT TEST PROTOCOL -- Wed Oct 18 17:23:11 2023 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ramr RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In foreach(chunk = chunks, .combine = c) %dorng% matrixStats::rowMedians(betas[chunk,  :
  Foreach loop (doParallelMC) had changed the current RNG type: RNG was restored to same type, next state
2: In foreach(chunk = chunks, .combine = c) %dorng% matrixStats::rowIQRs(betas[chunk,  :
  Foreach loop (doParallelMC) had changed the current RNG type: RNG was restored to same type, next state
3: In for (i in seq_len(n)) { :
  closing unused connection 10 (<-localhost:11932)
4: In for (i in seq_len(n)) { :
  closing unused connection 9 (<-localhost:11932)
5: In for (i in seq_len(n)) { :
  closing unused connection 8 (<-localhost:11932)
6: In for (i in seq_len(n)) { :
  closing unused connection 7 (<-localhost:11932)
7: In for (i in seq_len(n)) { :
  closing unused connection 6 (<-localhost:11932)
8: In for (i in seq_len(n)) { :
  closing unused connection 5 (<-localhost:11932)
9: In for (i in seq_len(n)) { :
  closing unused connection 4 (<-localhost:11932)
10: In foreach(column = colnames(betas.filtered)) %dorng% getMergedRanges(column) :
  Foreach loop (doParallelMC) had changed the current RNG type: RNG was restored to same type, next state
> 
> proc.time()
   user  system elapsed 
 61.602   3.809  72.228