##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ramr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ramr_1.17.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘ramr/DESCRIPTION’ ... OK
* this is package ‘ramr’ version ‘1.17.1’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
  Not all R platforms support C++20
* checking installed package size ... INFO
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.7Mb
* 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 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 14.581  1.455   9.535
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ramr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ramr
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ramr’ ...
** this is package ‘ramr’ version ‘1.17.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++20
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_compute_logp.cpp -o rcpp_compute_logp.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_compute_xiqr.cpp -o rcpp_compute_xiqr.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_create_granges.cpp -o rcpp_create_granges.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_filter_threshold.cpp -o rcpp_filter_threshold.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_fit_beta.cpp -o rcpp_fit_beta.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_fit_betabinom.cpp -o rcpp_fit_betabinom.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_fit_binom.cpp -o rcpp_fit_binom.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_generate_random_values.cpp -o rcpp_generate_random_values.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_get_iqr.cpp -o rcpp_get_iqr.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_get_meanvar.cpp -o rcpp_get_meanvar.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_helper_functions.cpp -o rcpp_helper_functions.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_prepare_data.cpp -o rcpp_prepare_data.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_test_omp.cpp -o rcpp_test_omp.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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.

> BiocGenerics:::testPackage("ramr")
Preprocessing data [0.094s]
Computing IQR [0.007s]
Creating genomic ranges [0.035s]
Preprocessing data [0.086s]
Computing IQR [0.003s]
Creating genomic ranges [0.014s]
Loading required namespace: GenomeInfoDb
Preprocessing data [0.089s]
Fitting beta distribution [0.095s]
Creating genomic ranges [0.015s]
Preprocessing data [0.085s]
Fitting beta distribution [0.110s]
Creating genomic ranges [0.014s]
Preprocessing data [0.091s]
Computing IQR [0.003s]
Creating genomic ranges [0.014s]
Preprocessing data [0.086s]
Computing IQR [0.007s]
Creating genomic ranges [0.014s]
Preprocessing data [0.084s]
Computing IQR [0.004s]
Creating genomic ranges [0.014s]
Preprocessing data [0.084s]
Fitting beta distribution [0.093s]
Creating genomic ranges [0.015s]
Preprocessing data [0.086s]
Computing IQR [0.007s]
Creating genomic ranges [0.018s]
Preprocessing data [0.084s]
Fitting beta distribution [0.093s]
Creating genomic ranges [0.015s]
Preprocessing data [0.086s]
Fitting beta distribution [0.114s]
Creating genomic ranges [0.020s]
Preprocessing data [0.089s]
Fitting beta distribution [0.110s]
Creating genomic ranges [0.020s]
Preprocessing data [0.105s]
Fitting beta distribution [0.111s]
Creating genomic ranges [0.026s]
Preprocessing data [0.090s]
Fitting beta distribution [0.098s]
Creating genomic ranges [0.015s]
Preprocessing data [0.084s]
Fitting beta distribution [0.105s]
Creating genomic ranges [0.015s]
Preprocessing data [0.127s]
Fitting beta distribution [0.116s]
Creating genomic ranges [0.023s]
Preprocessing data [0.091s]
Fitting beta distribution [0.066s]
Creating genomic ranges [0.025s]
Preprocessing data [0.089s]
Fitting beta distribution [0.060s]
Creating genomic ranges [0.026s]
Identifying AMRsLoading required package: foreach
Loading required package: rngtools
 [6.033s]
Identifying AMRs [4.251s]
Identifying AMRs [7.410s]
Identifying AMRs [7.433s]
Identifying AMRs [3.317s]
Identifying AMRs [75.877s]
Preprocessing data [0.097s]
Plotting 5 genomic ranges Plotting 5 genomic ranges  20% 40% 60% 80%100%[1.484s]
Plotting 6 genomic ranges  17% 33% 50% 67% 83%100%[0.967s]
'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 [0.095s]
Simulating data [0.005s]
Introducing epimutations[0.141s]
Preprocessing data [0.102s]
Simulating data [0.004s]
Introducing epimutations[0.072s]
Preprocessing data [0.103s]
Simulating data [0.041s]
Preprocessing data [0.089s]
Simulating data [0.042s]
Preprocessing data [0.086s]
Simulating data [0.041s]
Preprocessing data [0.096s]
Simulating data [0.039s]
Simulating data [0.992s]
Introducing epimutations [0.071s]
Simulating data [1.014s]
Introducing epimutations [0.070s]


RUNIT TEST PROTOCOL -- Sat Oct 25 03:12:04 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 
214.538   7.899 127.002