##############################################################################
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###
### 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ramr/DESCRIPTION’ ... OK
* this is package ‘ramr’ version ‘1.18.0’
* 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
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... OK
  Not all R platforms support C++20
* 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 whether startup messages can be suppressed ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getAMR.obsolete 17.054  1.312  16.304
plotAMR          5.716  0.185   8.342
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ramr
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ramr’ ...
** this is package ‘ramr’ version ‘1.18.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++20
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_compute_logp.cpp -o rcpp_compute_logp.o
rcpp_compute_logp.cpp:150:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_compute_xiqr.cpp -o rcpp_compute_xiqr.o
rcpp_compute_xiqr.cpp:37:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_create_granges.cpp -o rcpp_create_granges.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_filter_threshold.cpp -o rcpp_filter_threshold.o
rcpp_filter_threshold.cpp:32:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_fit_beta.cpp -o rcpp_fit_beta.o
rcpp_fit_beta.cpp:28:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_fit_betabinom.cpp -o rcpp_fit_betabinom.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_fit_binom.cpp -o rcpp_fit_binom.o
rcpp_fit_binom.cpp:33:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_generate_random_values.cpp -o rcpp_generate_random_values.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_get_iqr.cpp -o rcpp_get_iqr.o
rcpp_get_iqr.cpp:35:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_get_meanvar.cpp -o rcpp_get_meanvar.o
rcpp_get_meanvar.cpp:62:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_helper_functions.cpp -o rcpp_helper_functions.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_prepare_data.cpp -o rcpp_prepare_data.o
rcpp_prepare_data.cpp:87:16: warning: unused variable 'nthreads' [-Wunused-variable]
  const size_t nthreads = thr->size() - 1;                                      // 'thr' always starts with 0 and ends with 'nrow'
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_test_omp.cpp -o rcpp_test_omp.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ramr.so RcppExports.o rcpp_compute_logp.o rcpp_compute_xiqr.o rcpp_create_granges.o rcpp_filter_threshold.o rcpp_fit_beta.o rcpp_fit_betabinom.o rcpp_fit_binom.o rcpp_generate_random_values.o rcpp_get_iqr.o rcpp_get_meanvar.o rcpp_helper_functions.o rcpp_prepare_data.o rcpp_test_omp.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-ramr/00new/ramr/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> BiocGenerics:::testPackage("ramr")
Preprocessing data [0.126s]
Computing IQR [0.011s]
Creating genomic ranges [0.098s]
Preprocessing data [0.144s]
Computing IQR [0.011s]
Creating genomic ranges [0.015s]
Loading required namespace: GenomeInfoDb
Preprocessing data [0.172s]
Fitting beta distribution [0.276s]
Creating genomic ranges [0.021s]
Preprocessing data [0.144s]
Fitting beta distribution [0.255s]
Creating genomic ranges [0.036s]
Preprocessing data [0.113s]
Computing IQR [0.005s]
Creating genomic ranges [0.015s]
Preprocessing data [0.134s]
Computing IQR [0.024s]
Creating genomic ranges [0.027s]
Preprocessing data [0.092s]
Computing IQR [0.006s]
Creating genomic ranges [0.016s]
Preprocessing data [0.121s]
Fitting beta distribution [0.220s]
Creating genomic ranges [0.019s]
Preprocessing data [0.108s]
Computing IQR [0.046s]
Creating genomic ranges [0.026s]
Preprocessing data [0.169s]
Fitting beta distribution [0.208s]
Creating genomic ranges [0.032s]
Preprocessing data [0.122s]
Fitting beta distribution [0.253s]
Creating genomic ranges [0.015s]
Preprocessing data [0.136s]
Fitting beta distribution [0.240s]
Creating genomic ranges [0.032s]
Preprocessing data [0.127s]
Fitting beta distribution [0.248s]
Creating genomic ranges [0.023s]
Preprocessing data [0.138s]
Fitting beta distribution [0.200s]
Creating genomic ranges [0.017s]
Preprocessing data [0.113s]
Fitting beta distribution [0.268s]
Creating genomic ranges [0.023s]
Preprocessing data [0.132s]
Fitting beta distribution [0.254s]
Creating genomic ranges [0.025s]
Preprocessing data [0.129s]
Fitting beta distribution [0.155s]
Creating genomic ranges [0.032s]
Preprocessing data [0.101s]
Fitting beta distribution [0.143s]
Creating genomic ranges [0.021s]
Identifying AMRsLoading required package: foreach
Loading required package: rngtools
 [10.493s]
Identifying AMRs [6.003s]
Identifying AMRs [14.823s]
Identifying AMRs [13.002s]
Identifying AMRs [5.398s]
Identifying AMRs [147.893s]
Preprocessing data [0.147s]
Plotting 5 genomic ranges Plotting 5 genomic ranges  20% 40% 60% 80%100%[1.666s]
Plotting 6 genomic ranges  17% 33% 50% 67% 83%100%[1.547s]
'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
Preprocessing data [0.162s]
Simulating data [0.016s]
Introducing epimutations[0.096s]
Preprocessing data [0.122s]
Simulating data [0.010s]
Introducing epimutations[0.078s]
Preprocessing data [0.142s]
Simulating data [0.107s]
Preprocessing data [0.120s]
Simulating data [0.150s]
Preprocessing data [0.156s]
Simulating data [0.097s]
Preprocessing data [0.135s]
Simulating data [0.091s]
Simulating data [1.547s]
Introducing epimutations [0.109s]
Simulating data [1.581s]
Introducing epimutations [0.131s]


RUNIT TEST PROTOCOL -- Sat Nov 22 19:29:02 2025 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ramr RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In foreach::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::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 foreach::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 
251.469  17.734 233.893