##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:epigraHMM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epigraHMM_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/epigraHMM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigraHMM/DESCRIPTION’ ... OK
* this is package ‘epigraHMM’ version ‘1.16.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘epigraHMM’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
* 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 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 LazyData ... 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 ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/epigraHMM/libs/epigraHMM.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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
epigraHMMDataSetFromBam 17.628  3.835  67.484
callPatterns            17.116  0.387  25.717
plotPatterns            15.292  0.422  15.720
segmentGenome           14.505  0.617  33.087
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/epigraHMM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL epigraHMM
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘epigraHMM’ ...
** this is package ‘epigraHMM’ version ‘1.16.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c aggregate.cpp -o aggregate.o
aggregate.cpp: In function ‘arma::mat aggregate(arma::vec, arma::vec)’:
aggregate.cpp:26:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   26 |         while( index >= vec.size() ){
      |                ~~~~~~^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c computeBIC.cpp -o computeBIC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c computeQFunction.cpp -o computeQFunction.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c computeViterbiSequence.cpp -o computeViterbiSequence.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c expStep.cpp -o expStep.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c getMarginalProbability.cpp -o getMarginalProbability.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c innerMaxStepProb.cpp -o innerMaxStepProb.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c maxStepProb.cpp -o maxStepProb.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c rbinomVectorized.cpp -o rbinomVectorized.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c reweight.cpp -o reweight.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include   -fopenmp -DARMA_USE_HDF5 -fPIC  -g -O2  -Wall -Werror=format-security  -c simulateMarkovChain.cpp -o simulateMarkovChain.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o epigraHMM.so RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -fopenmp -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-epigraHMM/00new/epigraHMM/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (epigraHMM)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(epigraHMM)
> 
> test_check("epigraHMM")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 65 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
 96.100   2.743 144.450