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Package 57/514HostnameOS / ArchBUILDCHECKBUILD BIN
BHC 1.6.0
Rich Savage
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/BHC
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: BHC
Version: 1.6.0
Command: rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BHC.buildbin-libdir BHC_1.6.0.tar.gz >BHC-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=BHC.buildbin-libdir --install="check:BHC-install.out" --force-multiarch --no-vignettes --timings BHC_1.6.0.tar.gz && mv BHC.buildbin-libdir/* BHC.Rcheck/ && rmdir BHC.buildbin-libdir
StartedAt: 2012-03-24 00:34:36 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:36:01 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 84.8 seconds
RetCode: 0
Status:  OK  
CheckDir: BHC.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/BHC.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-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 '1.6.0'
* 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 whether package 'BHC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

BHC.Rcheck/00install.out:


install for i386

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

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


** libs
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c DataSet.cpp -o DataSet.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c MultinomialDataSet.cpp -o MultinomialDataSet.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c Node.cpp -o Node.o
Node.cpp:44:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
Node.cpp:104:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
SquaredExponentialTimecourseDataSet.cpp: In member function 'void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector<double>, double&, double&, double&, double)':
SquaredExponentialTimecourseDataSet.cpp:311:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable]
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c TimecourseDataSet.cpp -o TimecourseDataSet.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c bhc.cpp -o bhc.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c gammaln.cpp -o gammaln.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c header.cpp -o header.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -mtune=core2 -c multinomial_binevidence.cpp -o multinomial_binevidence.o
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 -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/BHC.buildbin-libdir/BHC/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'bhc.Rnw' 
** testing if installed package can be loaded

add DLL for x64

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

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


** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c DataSet.cpp -o DataSet.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c MultinomialDataSet.cpp -o MultinomialDataSet.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c Node.cpp -o Node.o
Node.cpp:44:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
Node.cpp:104:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
SquaredExponentialTimecourseDataSet.cpp: In member function 'void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector<double>, double&, double&, double&, double)':
SquaredExponentialTimecourseDataSet.cpp:311:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c TimecourseDataSet.cpp -o TimecourseDataSet.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c bhc.cpp -o bhc.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c gammaln.cpp -o gammaln.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c header.cpp -o header.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -m64 -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 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/BHC.buildbin-libdir/BHC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BHC' as BHC_1.6.0.zip

* DONE (BHC)