BHC 1.32.0
Rich Savage
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/BHC |
| Branch: RELEASE_3_7 |
| Last Commit: ee44b77 |
| Last Changed Date: 2018-04-30 10:35:14 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BHC_1.32.0.tar.gz && rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BHC.buildbin-libdir BHC_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BHC_1.32.0.zip && rm BHC_1.32.0.tar.gz BHC_1.32.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 81836 100 81836 0 0 1300k 0 --:--:-- --:--:-- --:--:-- 1453k
install for i386
* installing *source* package 'BHC' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16:0,
from BlockCovarianceMatrix.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16:0,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16:0,
from DataSet.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4:0,
from DirichletProcessMixture.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
DirichletProcessMixture.cpp:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
^
DirichletProcessMixture.cpp:272:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
^
DirichletProcessMixture.cpp:299:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1)
^
DirichletProcessMixture.cpp:375:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(j) schedule(dynamic,1)
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16:0,
from MultinomialDataSet.h:4,
from MultinomialDataSet.cpp:1:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Node.cpp -o Node.o
In file included from Node.h:16:0,
from Node.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16:0,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20:0,
from RobustSquaredExponentialTimecourseDataSet.h:20,
from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20:0,
from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: 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:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16:0,
from TimecourseDataSet.h:20,
from TimecourseDataSet.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:0:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c gammaln.cpp -o gammaln.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c header.cpp -o header.o
In file included from header.cpp:1:0:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_binevidence.cpp -o multinomial_binevidence.o
C:/Rtools/mingw_32/bin/g++ -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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/BHC.buildbin-libdir/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
In R CMD INSTALL
install for x64
* installing *source* package 'BHC' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16:0,
from BlockCovarianceMatrix.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16:0,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16:0,
from DataSet.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4:0,
from DirichletProcessMixture.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
DirichletProcessMixture.cpp:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
^
DirichletProcessMixture.cpp:272:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(i) schedule(dynamic,1)
^
DirichletProcessMixture.cpp:299:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1)
^
DirichletProcessMixture.cpp:375:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for default(shared) private(j) schedule(dynamic,1)
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16:0,
from MultinomialDataSet.h:4,
from MultinomialDataSet.cpp:1:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Node.cpp -o Node.o
In file included from Node.h:16:0,
from Node.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16:0,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20:0,
from RobustSquaredExponentialTimecourseDataSet.h:20,
from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20:0,
from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: 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:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16:0,
from TimecourseDataSet.h:20,
from TimecourseDataSet.cpp:13:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:0:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c gammaln.cpp -o gammaln.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c header.cpp -o header.o
In file included from header.cpp:1:0:
header.h:16:0: warning: "NDEBUG" redefined
#define NDEBUG
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c multinomial_binevidence.cpp -o multinomial_binevidence.o
C:/Rtools/mingw_64/bin/g++ -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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/BHC.buildbin-libdir/BHC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BHC' as BHC_1.32.0.zip
* DONE (BHC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BHC' successfully unpacked and MD5 sums checked
In R CMD INSTALL