##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeoDiff.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GeoDiff_1.14.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GeoDiff.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 'GeoDiff/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeoDiff' version '1.14.0'
* 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 'GeoDiff' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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/GeoDiff/libs/x64/GeoDiff.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
fitPoisthNorm-methods 63.38   0.62   64.03
fitNBthmDE-methods    19.44   0.46   19.91
fitNBthDE-methods     17.51   0.45   17.97
fitNBth-methods       13.58   0.51   14.09
QuanRange-methods      7.41   0.78    8.20
BGScoreTest-methods    4.89   0.19    5.08
* 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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/GeoDiff.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GeoDiff
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'GeoDiff' ...
** this is package 'GeoDiff' version '1.14.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++11
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c NBthDEOptPara.cpp -o NBthDEOptPara.o
NBthDEOptPara.cpp: In member function 'virtual double NBthDE_paranll::operator()(const arma::vec&)':
NBthDEOptPara.cpp:34:9: warning: unused variable 'm' [-Wunused-variable]
   34 |     int m = y.n_elem;
      |         ^
NBthDEOptPara.cpp: In member function 'virtual void NBthDE_paranll::Gradient(const arma::vec&, arma::vec&)':
NBthDEOptPara.cpp:85:22: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   85 |     for(int k = 0; k < y.n_elem; k++){
      |                    ~~^~~~~~~~~~
NBthDEOptPara.cpp:58:9: warning: unused variable 'm' [-Wunused-variable]
   58 |     int m = y.n_elem;
      |         ^
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c NBthmDEGrad.cpp -o NBthmDEGrad.o
NBthmDEGrad.cpp: In function 'arma::vec NBthmDE_grad(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::mat&, double, double)':
NBthmDEGrad.cpp:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   34 |   for(int i = 0; i < y.n_elem; i++){
      |                  ~~^~~~~~~~~~
NBthmDEGrad.cpp: In function 'arma::mat NBthmDE_gradM(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::mat&, arma::vec&, arma::vec&, arma::mat&, double, double)':
NBthmDEGrad.cpp:90:24: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
   90 |       for(int k = 0; k < y.n_elem; k++){
      |                      ~~^~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c NBthmDEMH.cpp -o NBthmDEMH.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o
NBthmDEOptPara.cpp: In member function 'virtual void NBthmDE_fparanll::Gradient(const arma::vec&, arma::vec&)':
NBthmDEOptPara.cpp:107:24: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
  107 |       for(int k = 0; k < y.n_elem; k++){
      |                      ~~^~~~~~~~~~
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c NBthmDEOptU.cpp -o NBthmDEOptU.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c PoisthNormOptPara.cpp -o PoisthNormOptPara.o
g++  -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/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++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/roptim/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o
g++ -shared -s -static-libgcc -o GeoDiff.dll tmp.def NBthDEOptPara.o NBthmDEGrad.o NBthmDEMH.o NBthmDEOptPara.o NBthmDEOptU.o PoisthNormOptPara.o RcppExports.o dnbinom_mu_vec.o -fopenmp -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lquadmath -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-GeoDiff/00new/GeoDiff/libs/x64
** R
** data
** 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 (GeoDiff)

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.

> library(testthat)
> library(GeoDiff)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(Biobase)
> 
> proc.time()
   user  system elapsed 
   9.18    0.67    9.81