| Back to Mac ARM64 build report for BioC 3.17 | 
  | 
This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 | 
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BHC 1.52.0  (landing page) Rich Savage 
  | kjohnson2 | macOS 12.6.1 Monterey / arm64 | ERROR | ERROR | skipped | skipped | ||||||||
| 
To the developers/maintainers of the BHC package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.  | 
| Package: BHC | 
| Version: 1.52.0 | 
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BHC | 
| StartedAt: 2023-10-15 21:40:37 -0400 (Sun, 15 Oct 2023) | 
| EndedAt: 2023-10-15 21:40:49 -0400 (Sun, 15 Oct 2023) | 
| EllapsedTime: 12.0 seconds | 
| RetCode: 1 | 
| Status: ERROR | 
| PackageFile: None | 
| PackageFileSize: NA | 
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BHC
###
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* checking for file ‘BHC/DESCRIPTION’ ... OK
* preparing ‘BHC’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘BHC’ ...
** using staged installation
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking for clang -arch arm64 option to support OpenMP... unsupported
configure: WARNING: No OpenMP support. If using GCC, upgrade to >= 4.2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.cpp:15:
In file included from ./BlockCovarianceMatrix.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from CubicSplineTimecourseDataSet.cpp:15:
In file included from ./CubicSplineTimecourseDataSet.h:20:
In file included from ./TimecourseDataSet.h:20:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
In file included from CubicSplineTimecourseDataSet.cpp:15:
./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual]
  double GetMLIINoise(const vector<int>& itemIndex);
         ^
./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector<int>' vs 'const vector<int> &')
  double GetMLIINoise(vector<int> itemIndex);
         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DataSet.cpp -o DataSet.o
In file included from DataSet.cpp:13:
In file included from ./DataSet.h:16:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
DataSet.cpp:36:48: warning: if statement has empty body [-Wempty-body]
    if(!system("PAUSE")) /* could not pause */ ;
                                               ^
DataSet.cpp:36:48: note: put the semicolon on a separate line to silence this warning
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.cpp:15:
In file included from ./DirichletProcessMixture.h:4:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
DirichletProcessMixture.cpp:164:12: error: no member named 'random_shuffle' in namespace 'std'
      std::random_shuffle(random_id.begin(), random_id.end());
      ~~~~~^
1 warning and 1 error generated.
make: *** [DirichletProcessMixture.o] Error 1
ERROR: compilation failed for package ‘BHC’
* removing ‘/private/tmp/RtmpJlt2G5/Rinst971040795283/BHC’
      -----------------------------------
ERROR: package installation failed