BioC 2.13: CHECK report for BHC on perceval

Package: BHC

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BHC_1.14.0.tar.gz

StartedAt: 2014-04-04 23:42:07 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:42:47 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 39.5 seconds

RetCode: 0

Status:  OK

CheckDir: BHC.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/BHC.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BHC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BHC’ version ‘1.14.0’
* 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 ... [18s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/BHC.Rcheck/BHC/libs/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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘bhc.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [7s/3s] OK
Examples with CPU or elapsed time > 5s
    user system elapsed
BHC 6.46  0.059   2.756
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/BHC.Rcheck/00check.log’
for details.

* installing *source* package ‘BHC’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking for llvm-gcc-4.2 -arch x86_64 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gammaln.cpp -o gammaln.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c multinomial_binevidence.cpp -o multinomial_binevidence.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/BHC.Rcheck/BHC/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BHC)

name	user	system	elapsed
BHC	6.460	0.059	2.756