Multiple platform build/check report for BioC 3.11

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BHC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BHC_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BHC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BHC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BHC' version '1.40.0'
* 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 'BHC' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
FindOptimalHyperparameter: no visible global function definition for
  'optimise'
WriteOutClusterLabels : WhereToCut: no visible global function
  definition for 'is.leaf'
WriteOutClusterLabels: no visible global function definition for
  'dendrapply'
WriteOutClusterLabels: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  dendrapply is.leaf optimise write.table
Consider adding
  importFrom("stats", "dendrapply", "is.leaf", "optimise")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 shell scripts ... 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BHC/libs/i386/BHC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BHC/libs/x64/BHC.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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. 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/BHC.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/BHC_1.40.0.tar.gz && rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BHC.buildbin-libdir BHC_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BHC_1.40.0.zip && rm BHC_1.40.0.tar.gz BHC_1.40.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 81827  100 81827    0     0  1503k      0 --:--:-- --:--:-- --:--:-- 1737k

install for i386

* installing *source* package 'BHC' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16,
                 from BlockCovarianceMatrix.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16,
                 from DataSet.cpp:13:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4,
                 from DirichletProcessMixture.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
DirichletProcessMixture.cpp:187: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
 
DirichletProcessMixture.cpp:272: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
 
DirichletProcessMixture.cpp:299: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1)
 
DirichletProcessMixture.cpp:375: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(j) schedule(dynamic,1)
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16,
                 from MultinomialDataSet.h:4,
                 from MultinomialDataSet.cpp:1:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Node.cpp -o Node.o
In file included from Node.h:16,
                 from Node.cpp:13:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
                 from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
SquaredExponentialTimecourseDataSet.cpp: In member function 'void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector<double>, double&, double&, double&, double)':
SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable]
   double currentLogEvidence, gridLogEvidence,
                              ^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from TimecourseDataSet.cpp:13:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gammaln.cpp -o gammaln.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c header.cpp -o header.o
In file included from header.cpp:1:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_binevidence.cpp -o multinomial_binevidence.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BHC.dll tmp.def BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BHC'
    finding HTML links ... done
    BHC                                     html  
** 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

install for x64

* installing *source* package 'BHC' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16,
                 from BlockCovarianceMatrix.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16,
                 from DataSet.cpp:13:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4,
                 from DirichletProcessMixture.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
DirichletProcessMixture.cpp:187: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
 
DirichletProcessMixture.cpp:272: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
 
DirichletProcessMixture.cpp:299: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1)
 
DirichletProcessMixture.cpp:375: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for default(shared) private(j) schedule(dynamic,1)
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16,
                 from MultinomialDataSet.h:4,
                 from MultinomialDataSet.cpp:1:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Node.cpp -o Node.o
In file included from Node.h:16,
                 from Node.cpp:13:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from CubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.h:20,
                 from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.h:20,
                 from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
                 from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
SquaredExponentialTimecourseDataSet.cpp: In member function 'void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector<double>, double&, double&, double&, double)':
SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable]
   double currentLogEvidence, gridLogEvidence,
                              ^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16,
                 from TimecourseDataSet.h:20,
                 from TimecourseDataSet.cpp:13:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gammaln.cpp -o gammaln.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c header.cpp -o header.o
In file included from header.cpp:1:
header.h:16: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c multinomial_binevidence.cpp -o multinomial_binevidence.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BHC.dll tmp.def BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/BHC.buildbin-libdir/BHC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BHC' as BHC_1.40.0.zip
* DONE (BHC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BHC' successfully unpacked and MD5 sums checked

CHECK report for BHC on tokay2

Summary

Command output

Installation output

Tests output

Example timings