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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:DifferentialRegulation.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DifferentialRegulation_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DifferentialRegulation.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DifferentialRegulation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DifferentialRegulation’ version ‘2.4.0’
* 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 ‘DifferentialRegulation’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      3.3Mb
* 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 ... NOTE
MCMC_ECs: no visible binding for global variable ‘cl’
Undefined global functions or variables:
  cl
* checking Rd files ... NOTE
checkRd: (-1) DifferentialRegulation.Rd:159: Lost braces
   159 | \code{\link{load_EC}}, \code{\link{load_USA}}, code{\link{compute_PB_counts}}, \code{\link{plot_pi}}, \code{\link{plot_traceplot}}
       |                                                    ^
* 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 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
DifferentialRegulation_bulk 484.718 2168.569 1423.666
DifferentialRegulation        5.383    0.264   22.710
load_bulk_EC                  0.187    0.033   13.588
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testhat.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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DifferentialRegulation.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL DifferentialRegulation
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* installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’
* installing *source* package ‘DifferentialRegulation’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.3/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.3/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.3/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.3/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Rcpp_MCMC.cpp -o Rcpp_MCMC.o
Rcpp_MCMC.cpp: In function ‘Rcpp::NumericVector Rcpp_MCMC(const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const Rcpp::IntegerVector&, const Rcpp::IntegerVector&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::IntegerVector&, const unsigned int&, const unsigned int&, Rcpp::NumericMatrix&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::NumericMatrix&, const Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<13> > >&, const Rcpp::ListOf<Rcpp::Vector<13> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::IntegerVector&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::IntegerVector&, const double&)’:
Rcpp_MCMC.cpp:305:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const Rcpp::traits::storage_type<13>::type’ {aka ‘const int’} [-Wsign-compare]
  305 |         for(sample = 0; sample < n_samples_per_group[ gr ]; sample ++){
Rcpp_MCMC.cpp:135:10: warning: unused variable ‘tmp_1’ [-Wunused-variable]
  135 |   double tmp_1, tmp_2, tmp_3;
      |          ^~~~~
Rcpp_MCMC.cpp:135:17: warning: unused variable ‘tmp_2’ [-Wunused-variable]
  135 |   double tmp_1, tmp_2, tmp_3;
      |                 ^~~~~
Rcpp_MCMC.cpp:135:24: warning: unused variable ‘tmp_3’ [-Wunused-variable]
  135 |   double tmp_1, tmp_2, tmp_3;
      |                        ^~~~~
Rcpp_MCMC.cpp:394:10: warning: ‘ll_original’ may be used uninitialized [-Wmaybe-uninitialized]
  394 |       ll += ll_original;
      |       ~~~^~~~~~~~~~~~~~
Rcpp_MCMC.cpp:296:21: note: ‘ll_original’ was declared here
  296 |     double ll_prop, ll_original, ll = 0;
      |                     ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.3/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.3/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.3/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Rcpp_MCMC_EC_US.cpp -o Rcpp_MCMC_EC_US.o
Rcpp_MCMC_EC_US.cpp: In function ‘Rcpp::NumericVector Rcpp_MCMC_EC_US(const unsigned int&, const unsigned int&, const unsigned int&, const unsigned int&, const Rcpp::IntegerVector&, const Rcpp::IntegerVector&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::IntegerVector&, const unsigned int&, const unsigned int&, Rcpp::NumericMatrix&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::NumericMatrix&, const Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<13> > >&, const Rcpp::ListOf<Rcpp::Vector<13> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const Rcpp::IntegerVector&, const Rcpp::IntegerVector&, const Rcpp::NumericVector&, const Rcpp::NumericVector&, const double&)’:
Rcpp_MCMC_EC_US.cpp:310:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const Rcpp::traits::storage_type<13>::type’ {aka ‘const int’} [-Wsign-compare]
  310 |         for(sample = 0; sample < n_samples_per_group[ gr ]; sample ++){
Rcpp_MCMC_EC_US.cpp:130:10: warning: unused variable ‘tmp_1’ [-Wunused-variable]
  130 |   double tmp_1, tmp_2, tmp;
      |          ^~~~~
Rcpp_MCMC_EC_US.cpp:130:17: warning: unused variable ‘tmp_2’ [-Wunused-variable]
  130 |   double tmp_1, tmp_2, tmp;
      |                 ^~~~~
Rcpp_MCMC_EC_US.cpp:399:12: warning: ‘ll_original’ may be used uninitialized [-Wmaybe-uninitialized]
  399 |         ll += ll_original;
      |         ~~~^~~~~~~~~~~~~~
Rcpp_MCMC_EC_US.cpp:290:21: note: ‘ll_original’ was declared here
  290 |     double ll_prop, ll_original, ll = 0;
      |                     ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.3/lib -L/usr/local/lib -o DifferentialRegulation.so RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_EC_US.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.4.3/lib -lR
installing to /home/biocbuild/R/R-4.4.3/site-library/00LOCK-DifferentialRegulation/00new/DifferentialRegulation/libs
** R
** 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 (DifferentialRegulation)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
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(DifferentialRegulation)
> test_check("DifferentialRegulation")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 13.462   0.591  27.159