##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ramr.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ramr_1.16.0.tar.gz
###
##############################################################################
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ramr.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ramr/DESCRIPTION' ... OK
* this is package 'ramr' version '1.16.0'
* 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 whether package 'ramr' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/ramr/libs/x64/ramr.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotAMR               5.02   0.20    5.21
getAMR.obsolete       2.62   0.17   15.08
simulateData.obsolete 1.03   0.08    6.33
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/ramr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ramr
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'ramr' ...
** this is package 'ramr' version '1.16.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++20
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_compute_logp.cpp -o rcpp_compute_logp.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_compute_xiqr.cpp -o rcpp_compute_xiqr.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_create_granges.cpp -o rcpp_create_granges.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_filter_threshold.cpp -o rcpp_filter_threshold.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_fit_beta.cpp -o rcpp_fit_beta.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_fit_betabinom.cpp -o rcpp_fit_betabinom.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_fit_binom.cpp -o rcpp_fit_binom.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_generate_random_values.cpp -o rcpp_generate_random_values.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_get_iqr.cpp -o rcpp_get_iqr.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_get_meanvar.cpp -o rcpp_get_meanvar.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_helper_functions.cpp -o rcpp_helper_functions.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_prepare_data.cpp -o rcpp_prepare_data.o
g++  -std=gnu++20 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c rcpp_test_omp.cpp -o rcpp_test_omp.o
g++ -shared -s -static-libgcc -o ramr.dll tmp.def 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 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-ramr/00new/ramr/libs/x64
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 [0.110s]
Computing IQR [0.000s]
Creating genomic ranges [0.060s]
Preprocessing data [0.120s]
Computing IQR [0.000s]
Creating genomic ranges [0.020s]
Preprocessing data [0.140s]
Fitting beta distribution [0.110s]
Creating genomic ranges [0.030s]
Preprocessing data [0.130s]
Fitting beta distribution [0.140s]
Creating genomic ranges [0.020s]
Preprocessing data [0.110s]
Computing IQR [0.020s]
Creating genomic ranges [0.010s]
Preprocessing data [0.120s]
Computing IQR [0.020s]
Creating genomic ranges [0.020s]
Preprocessing data [0.140s]
Computing IQR [0.000s]
Creating genomic ranges [0.030s]
Preprocessing data [0.120s]
Fitting beta distribution [0.130s]
Creating genomic ranges [0.010s]
Preprocessing data [0.090s]
Computing IQR [0.000s]
Creating genomic ranges [0.020s]
Preprocessing data [0.070s]
Fitting beta distribution [0.110s]
Creating genomic ranges [0.030s]
Preprocessing data [0.150s]
Fitting beta distribution [0.150s]
Creating genomic ranges [0.020s]
Preprocessing data [0.130s]
Fitting beta distribution [0.120s]
Creating genomic ranges [0.030s]
Preprocessing data [0.100s]
Fitting beta distribution [0.120s]
Creating genomic ranges [0.020s]
Preprocessing data [0.100s]
Fitting beta distribution [0.120s]
Creating genomic ranges [0.020s]
Preprocessing data [0.090s]
Fitting beta distribution [0.130s]
Creating genomic ranges [0.060s]
Preprocessing data [0.110s]
Fitting beta distribution [0.160s]
Creating genomic ranges [0.030s]
Preprocessing data [0.100s]
Fitting beta distribution [0.090s]
Creating genomic ranges [0.050s]
Preprocessing data [0.120s]
Fitting beta distribution [0.110s]
Creating genomic ranges [0.050s]
Identifying AMRs [11.890s]
Identifying AMRs [9.030s]
Identifying AMRs [13.380s]
Identifying AMRs [13.370s]
Identifying AMRs [7.980s]
Identifying AMRs [113.200s]
Preprocessing data [0.120s]
Plotting 5 genomic ranges Plotting 5 genomic ranges  20% 40% 60% 80%100%[0.830s]
Plotting 6 genomic ranges  17% 33% 50% 67% 83%100%[0.860s]
'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 [0.110s]
Simulating data [0.000s]
Introducing epimutations[0.060s]
Preprocessing data [0.070s]
Simulating data [0.000s]
Introducing epimutations[0.050s]
Preprocessing data [0.080s]
Simulating data [0.070s]
Preprocessing data [0.070s]
Simulating data [0.100s]
Preprocessing data [0.080s]
Simulating data [0.080s]
Preprocessing data [0.070s]
Simulating data [0.080s]
Simulating data [6.700s]
Introducing epimutations [0.070s]
Simulating data [4.860s]
Introducing epimutations [0.050s]


RUNIT TEST PROTOCOL -- Fri Aug 15 05:55:46 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 
> 
> proc.time()
   user  system elapsed 
  23.32    1.60  202.85