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INSTALL report for BHC on malbec1

This page was generated on 2020-10-25 12:01:11 -0400 (Sun, 25 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BHC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 144/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BHC 1.41.0
Rich Savage
Snapshot Date: 2020-10-24 14:40:19 -0400 (Sat, 24 Oct 2020)
URL: https://git.bioconductor.org/packages/BHC
Branch: master
Last Commit: b561cae
Last Changed Date: 2020-04-27 14:22:27 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BHC
Version: 1.41.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BHC
StartedAt: 2020-10-24 16:25:04 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 16:25:27 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 23.8 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BHC
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BHC’ ...
** using staged installation
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to support OpenMP... -fopenmp
checking whether OpenMP will work in this package... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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,
                              ^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c gammaln.cpp -o gammaln.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/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 -fopenmp -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-BHC/00new/BHC/libs
** R
** 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)