BHC 1.11.0
Rich Savage
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BHC | | Last Changed Rev: 70052 / Revision: 74774 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BHC.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BHC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BHC' version '1.11.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BHC' can be installed ... [26s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/BHC.Rcheck/BHC/libs/i386/BHC.so':
Found '__ZSt4cout', possibly from 'std::cout' (C++)
Objects: 'BlockCovarianceMatrix.o',
'CubicSplineTimecourseDataSet.o', 'DataSet.o',
'DirichletProcessMixture.o', 'MultinomialDataSet.o', 'Node.o',
'RobustCubicSplineTimecourseDataSet.o',
'SquaredExponentialTimecourseDataSet.o', 'TimecourseDataSet.o',
'bhc.o', 'multinomial_OutputDendrogramInformation.o',
'multinomial_ReadInData.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [172s/35s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BHC 169.409 1.893 34.606
* 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
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/BHC.Rcheck/00check.log'
for details.
* installing *source* package 'BHC' ...
checking for gcc... gcc -arch i386 -std=gnu99
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 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking for gcc -arch i386 -std=gnu99 option to support OpenMP... -fopenmp
checking whether OpenMP will work in this package... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o
In file included from BlockCovarianceMatrix.h:16,
from BlockCovarianceMatrix.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c DataSet.cpp -o DataSet.o
In file included from DataSet.h:16,
from DataSet.cpp:13:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o
In file included from DirichletProcessMixture.h:4,
from DirichletProcessMixture.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c MultinomialDataSet.cpp -o MultinomialDataSet.o
In file included from DataSet.h:16,
from MultinomialDataSet.h:4,
from MultinomialDataSet.cpp:1:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c Node.cpp -o Node.o
In file included from Node.h:16,
from Node.cpp:13:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o
In file included from DataSet.h:16,
from TimecourseDataSet.h:20,
from CubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.h:20,
from RobustCubicSplineTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
from RobustSquaredExponentialTimecourseDataSet.h:20,
from RobustSquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o
In file included from SquaredExponentialTimecourseDataSet.h:20,
from SquaredExponentialTimecourseDataSet.cpp:15:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c TimecourseDataSet.cpp -o TimecourseDataSet.o
In file included from DataSet.h:16,
from TimecourseDataSet.h:20,
from TimecourseDataSet.cpp:13:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c bhc.cpp -o bhc.o
In file included from bhc.cpp:17:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c gammaln.cpp -o gammaln.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c header.cpp -o header.o
In file included from header.cpp:1:
header.h:16:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -fopenmp -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BHC.Rcheck/BHC/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'bhc.Rnw'
** testing if installed package can be loaded
* DONE (BHC)