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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DifferentialRegulation.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DifferentialRegulation_1.3.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/DifferentialRegulation.Rcheck'
* using R Under development (unstable) (2023-01-10 r83596 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DifferentialRegulation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DifferentialRegulation' version '1.3.0'
* 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 'DifferentialRegulation' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 R 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 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'
MCMC_USA: no visible binding for global variable 'cl'
Undefined global functions or variables:
  cl
* 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 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 'F:/biocbuild/bbs-3.17-bioc/R/library/DifferentialRegulation/libs/x64/DifferentialRegulation.dll':
  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
load_EC                2.46   1.55    8.53
DifferentialRegulation 3.02   0.26   15.50
plot_pi                1.83   0.01   13.76
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testhat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/DifferentialRegulation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DifferentialRegulation
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'DifferentialRegulation' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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::ListOf<Rcpp::Matrix<14> >&, const Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<13> > >&, const Rcpp::ListOf<Rcpp::ListOf<Rcpp::Vector<14, Rcpp::PreserveStorage> > >&, const Rcpp::ListOf<Rcpp::Vector<13> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::ListOf<Rcpp::Matrix<14> > >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const bool&, const double&, const double&, const double&)':
Rcpp_MCMC.cpp:279:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const Rcpp::traits::storage_type<13>::type' {aka 'const int'} [-Wsign-compare]
  279 |         for(sample = 0; sample < n_samples_per_group[ gr ]; sample ++){
Rcpp_MCMC.cpp:144:10: warning: unused variable 'tmp_1' [-Wunused-variable]
  144 |   double tmp_1, tmp_2, tmp_3;
      |          ^~~~~
Rcpp_MCMC.cpp:144:17: warning: unused variable 'tmp_2' [-Wunused-variable]
  144 |   double tmp_1, tmp_2, tmp_3;
      |                 ^~~~~
Rcpp_MCMC.cpp:144:24: warning: unused variable 'tmp_3' [-Wunused-variable]
  144 |   double tmp_1, tmp_2, tmp_3;
      |                        ^~~~~
Rcpp_MCMC.cpp:365:10: warning: 'll_original' may be used uninitialized [-Wmaybe-uninitialized]
  365 |       ll += ll_original;
      |       ~~~^~~~~~~~~~~~~~
Rcpp_MCMC.cpp:270:21: note: 'll_original' was declared here
  270 |     double ll_prop, ll_original, ll = 0;
      |                     ^~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rcpp_MCMC_sce.cpp -o Rcpp_MCMC_sce.o
Rcpp_MCMC_sce.cpp: In function 'Rcpp::NumericVector Rcpp_MCMC_sce(const unsigned int&, const unsigned int&, const unsigned int&, const Rcpp::IntegerVector&, const Rcpp::ListOf<Rcpp::Vector<13> >&, const Rcpp::IntegerVector&, const unsigned int&, const unsigned int&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, Rcpp::ListOf<Rcpp::ListOf<Rcpp::Matrix<14> > >&, Rcpp::ListOf<Rcpp::Matrix<14> >&, const bool&, const double&, const double&, const double&)':
Rcpp_MCMC_sce.cpp:234:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const Rcpp::traits::storage_type<13>::type' {aka 'const int'} [-Wsign-compare]
  234 |         for(sample = 0; sample < n_samples_per_group[ gr ]; sample ++){
Rcpp_MCMC_sce.cpp:145:10: warning: unused variable 'tmp_1' [-Wunused-variable]
  145 |   double tmp_1, tmp_2, tmp_3;
      |          ^~~~~
Rcpp_MCMC_sce.cpp:145:17: warning: unused variable 'tmp_2' [-Wunused-variable]
  145 |   double tmp_1, tmp_2, tmp_3;
      |                 ^~~~~
Rcpp_MCMC_sce.cpp:145:24: warning: unused variable 'tmp_3' [-Wunused-variable]
  145 |   double tmp_1, tmp_2, tmp_3;
      |                        ^~~~~
Rcpp_MCMC_sce.cpp:320:10: warning: 'll_original' may be used uninitialized [-Wmaybe-uninitialized]
  320 |       ll += ll_original;
      |       ~~~^~~~~~~~~~~~~~
Rcpp_MCMC_sce.cpp:227:21: note: 'll_original' was declared here
  227 |     double ll_prop, ll_original, ll = 0;
      |                     ^~~~~~~~~~~
g++ -shared -s -static-libgcc -o DifferentialRegulation.dll tmp.def RcppExports.o Rcpp_MCMC.o Rcpp_MCMC_sce.o -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-DifferentialRegulation/00new/DifferentialRegulation/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DifferentialRegulation)

R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 9 ]
> 
> proc.time()
   user  system elapsed 
  12.64    2.54   32.40