Package: birta

Version: 1.2.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings birta_1.2.0.tar.gz

StartedAt: 2013-03-24 23:44:44 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:45:43 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 58.8 seconds

RetCode: 0

Status:  OK

CheckDir: birta.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/birta.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘birta/DESCRIPTION’ ... OK
* this is package ‘birta’ version ‘1.2.0’
* 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 ‘birta’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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

* installing *source* package ‘birta’ ...
** libs
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BayesNetwork.cpp -o BayesNetwork.o
BayesNetwork.cpp: In constructor ‘BayesNetwork::BayesNetwork(int, int, int, char**, char**, char**, int**, double***, double***, int, int, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, double, double, double, double*, double*, double**, double**, double*, double*, int, double**, int, std::list<int>*, std::list<int>*, double, double, int, int, double, double, double, int**, int**, double***, int, double*, double*, double*, double, double, int**)’:
BayesNetwork.cpp:237:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:241:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp: In destructor ‘virtual BayesNetwork::˜BayesNetwork()’:
BayesNetwork.cpp:250:10: warning: unused variable ‘j’ [-Wunused-variable]
BayesNetwork.cpp: In member function ‘virtual double* BayesNetwork::MCMC(long int, long int, int)’:
BayesNetwork.cpp:868:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:963:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:1044:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:1140:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetwork.cpp:740:92: warning: ‘mu0’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BayesNetworkNC.cpp -o BayesNetworkNC.o
BayesNetworkNC.cpp: In member function ‘virtual double* BayesNetworkNC::MCMC(long int, long int, int)’:
BayesNetworkNC.cpp:465:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetworkNC.cpp:560:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetworkNC.cpp:640:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
BayesNetworkNC.cpp:735:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c getStates.cpp -o getStates.o
g++ -shared -L/usr/local/lib64 -o birta.so BayesNetwork.o BayesNetworkNC.o getStates.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/birta.Rcheck/birta/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘birta.Rnw’ 
** testing if installed package can be loaded

* DONE (birta)

name	user	system	elapsed
birta.run	2.868	0.044	3.234
get_potential_swaps	0.000	0.000	0.001
limmaAnalysis	0.164	0.000	0.166
plotConvergence	3.132	0.008	3.199