BioC 3.2: CHECK report for birte on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings birte_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/birte.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘birte/DESCRIPTION’ ... OK
* this is package ‘birte’ version ‘1.4.0’
* 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 ‘birte’ 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 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘birte/libs/birte.so’:
  Found ‘__ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘BayesNetwork.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [67s/67s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
birteFitRidge 17.324  0.194  17.567
birteRun      15.617  0.257  15.923
birtePredict  14.796  0.208  15.014
simulateData  14.207  0.107  14.317
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/birte.Rcheck/00check.log’
for details.

* installing *source* package ‘birte’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:
BayesNetwork.h:203:3: warning: "/*" within comment
BayesNetwork.cpp: In constructor ‘BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::list<int, std::allocator<int> >*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)’:
BayesNetwork.cpp:96: warning: unused variable ‘j’
BayesNetwork.cpp:96: warning: unused variable ‘r’
BayesNetwork.cpp: In destructor ‘virtual BayesNetwork::˜BayesNetwork()’:
BayesNetwork.cpp:221: warning: unused variable ‘i’
BayesNetwork.cpp:221: warning: unused variable ‘j’
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::list<int, std::allocator<int> >*, double**, int)’:
BayesNetwork.cpp:357: warning: unused variable ‘found’
BayesNetwork.cpp:357: warning: unused variable ‘i’
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)’:
BayesNetwork.cpp:380: warning: unused variable ‘k’
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)’:
BayesNetwork.cpp:599: warning: comparison between signed and unsigned integer expressions
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::swap_states(int**, int, int, std::set<int, std::less<int>, std::allocator<int> >*, std::list<int, std::allocator<int> >*, std::set<int, std::less<int>, std::allocator<int> >**, double)’:
BayesNetwork.cpp:669: warning: comparison between signed and unsigned integer expressions
BayesNetwork.cpp:665: warning: unused variable ‘pos_swaps’
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::MCMC(long int, long int, int, double*)’:
BayesNetwork.cpp:842: warning: unused variable ‘mir’
BayesNetwork.cpp:842: warning: unused variable ‘tf’
BayesNetwork.cpp:847: warning: unused variable ‘eff_samples’
BayesNetwork.cpp:909: warning: unused variable ‘u’
BayesNetwork.cpp:909: warning: unused variable ‘delta_prior’
BayesNetwork.cpp:909: warning: unused variable ‘eps_new’
BayesNetwork.cpp:909: warning: unused variable ‘eps_old’
BayesNetwork.cpp:909: warning: unused variable ‘delta_eps’
BayesNetwork.cpp:910: warning: unused variable ‘make_move_eps’
BayesNetwork.cpp:910: warning: unused variable ‘cond’
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::likelihood()’:
BayesNetwork.cpp:1074: warning: unused variable ‘j’
BayesNetwork.cpp:1075: warning: unused variable ‘bn’
BayesNetwork.cpp:1078: warning: unused variable ‘z’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:
BayesNetwork.h:203:3: warning: "/*" within comment
Loading required package: Rcpp
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Loading required package: Rcpp
installing to /Users/biocbuild/bbs-3.2-bioc/meat/birte.Rcheck/birte/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (birte)

name	user	system	elapsed
birteFitRidge	17.324	0.194	17.567
birtePredict	14.796	0.208	15.014
birteRun	15.617	0.257	15.923
estimateNetwork	0.001	0.000	0.001
getPotentialSwaps	0.698	0.053	0.752
limmaAnalysis	0.001	0.000	0.001
plotConvergence	0.001	0.000	0.000
proposeInteractions	0.228	0.005	0.233
simplify	0.116	0.004	0.120
simulateData	14.207	0.107	14.317
suggestThreshold	0.423	0.005	0.429

BioC 3.2: CHECK report for birte on perceval

Summary

Command output