BioC 3.6: CHECK report for BHC on malbec1

Package: BHC

Version: 1.29.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BHC_1.29.0.tar.gz

StartedAt: 2017-08-15 21:28:26 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:29:01 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 35.5 seconds

RetCode: 0

Status:  OK

CheckDir: BHC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BHC_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BHC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.29.0’
* 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 ... 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 loading without being on the library search path ... 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 ... NOTE
FindOptimalHyperparameter: no visible global function definition for
  ‘optimise’
WriteOutClusterLabels : WhereToCut: no visible global function
  definition for ‘is.leaf’
WriteOutClusterLabels: no visible global function definition for
  ‘dendrapply’
WriteOutClusterLabels: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  dendrapply is.leaf optimise write.table
Consider adding
  importFrom("stats", "dendrapply", "is.leaf", "optimise")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘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’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘DirichletProcessMixture.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘DirichletProcessMixture.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
    user system elapsed
BHC 5.32  0.024    1.66
* 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BHC.Rcheck/00check.log’
for details.

* installing *source* package ‘BHC’ ...
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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c gammaln.cpp -o gammaln.o
g++  -I/home/biocbuild/bbs-3.6-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++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -fopenmp  -I/usr/local/include   -fpic  -g -O2  -Wall -c multinomial_binevidence.cpp -o multinomial_binevidence.o
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	5.320	0.024	1.660