Rich Savage
| Snapshot Date: 2023-03-13 13:00:01 -0400 (Mon, 13 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/BHC |
| git_branch: master |
| git_last_commit: 314c29c |
| git_last_commit_date: 2022-11-01 11:05:08 -0400 (Tue, 01 Nov 2022) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-03-16 11:01:56 -0400 (Thu, 16 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4115 |
| 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 | ||||
|
To the developers/maintainers of the BHC package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 158/2189 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BHC 1.51.0 (landing page) Rich Savage
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
| Package: BHC |
| Version: 1.51.0 |
| Command: rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BHC.buildbin-libdir |
| StartedAt: 2023-03-14 14:37:33 -0400 (Tue, 14 Mar 2023) |
| EndedAt: 2023-03-14 14:37:50 -0400 (Tue, 14 Mar 2023) |
| EllapsedTime: 17.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BHC_1.51.0.tgz |
| PackageFileSize: 252.7 KiB |
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###
### Running command:
###
### rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.51.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BHC.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BHC.buildbin-libdir BHC_1.51.0.tar.gz'
>>>>>>>
* 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: ‘MacOSX13.0.sdk’
clang++ -arch arm64 -std=gnu++14 -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++14 -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++14 -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++14 -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: warning: 'random_shuffle<std::__wrap_iter<int *>>' is deprecated [-Wdeprecated-declarations]
std::random_shuffle(random_id.begin(), random_id.end());
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle<std::__wrap_iter<int *>>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
# define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from MultinomialDataSet.cpp:1:
In file included from ./MultinomialDataSet.h:4:
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 MultinomialDataSet.cpp:1:
./MultinomialDataSet.h:19:10: warning: 'MultinomialDataSet::SingleClusterLogEvidence' hides overloaded virtual function [-Woverloaded-virtual]
double SingleClusterLogEvidence(vector<int> itemIndex); // returns the log-evidence for a cluster that contains data items defined by itemIndex
^
./DataSet.h:29:18: note: hidden overloaded virtual function 'DataSet::SingleClusterLogEvidence' declared here: different number of parameters (5 vs 1)
virtual double SingleClusterLogEvidence(const vector<int>& itemIndex,
^
MultinomialDataSet.cpp:77:43: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE"))/* didn't pause */;
^
MultinomialDataSet.cpp:77:43: note: put the semicolon on a separate line to silence this warning
3 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Node.cpp -o Node.o
In file included from Node.cpp:13:
In file included from ./Node.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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from RobustCubicSplineTimecourseDataSet.cpp:15:
In file included from ./RobustCubicSplineTimecourseDataSet.h:20:
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 RobustCubicSplineTimecourseDataSet.cpp:15:
In file included from ./RobustCubicSplineTimecourseDataSet.h:20:
./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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from RobustSquaredExponentialTimecourseDataSet.cpp:15:
In file included from ./RobustSquaredExponentialTimecourseDataSet.h:20:
In file included from ./SquaredExponentialTimecourseDataSet.h:20:
./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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.cpp:15:
In file included from ./SquaredExponentialTimecourseDataSet.h:20:
./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG
^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
^
SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable]
double currentLogEvidence, gridLogEvidence,
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from TimecourseDataSet.cpp:13:
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
^
TimecourseDataSet.cpp:80:40: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE"))/*didn't work*/;
^
TimecourseDataSet.cpp:80:40: note: put the semicolon on a separate line to silence this warning
TimecourseDataSet.cpp:143:40: warning: if statement has empty body [-Wempty-body]
if(!system("PAUSE"))/*didn't work*/;
^
TimecourseDataSet.cpp:143:40: note: put the semicolon on a separate line to silence this warning
3 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
./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 bhc.cpp:20:
./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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gammaln.cpp -o gammaln.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c header.cpp -o header.o
In file included from header.cpp:1:
./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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_binevidence.cpp -o multinomial_binevidence.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BHC.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/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 (BHC)
>>>>>>>
>>>>>>> FIXING LINKS FOR BHC.buildbin-libdir/BHC/libs/BHC.so
>>>>>>>
install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "BHC.buildbin-libdir/BHC/libs/BHC.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "BHC.buildbin-libdir/BHC/libs/BHC.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "BHC.buildbin-libdir/BHC/libs/BHC.so"