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This page was generated on 2015-10-09 09:37:18 -0700 (Fri, 09 Oct 2015).
| Package 109/1024 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| birte 1.2.0 Holger Froehlich
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | | |||||
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| Package: birte |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings birte_1.2.0.tar.gz |
| StartedAt: 2015-10-08 21:45:15 -0700 (Thu, 08 Oct 2015) |
| EndedAt: 2015-10-08 21:47:58 -0700 (Thu, 08 Oct 2015) |
| EllapsedTime: 162.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: birte.Rcheck |
| Warnings: 0 |
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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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.2.0’
* 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 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 ... [25s/26s] 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 ... [64s/64s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
birteFitRidge 14.772 0.130 14.910
birtePredict 14.706 0.120 14.844
birteRun 14.640 0.170 14.824
simulateData 13.700 0.092 13.805
* 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-3.1-bioc/meat/birte.Rcheck/00check.log’
for details.
birte.Rcheck/00install.out:
* 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-3.1-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)
birte.Rcheck/birte-Ex.timings:
| name | user | system | elapsed | |
| birteFitRidge | 14.772 | 0.130 | 14.910 | |
| birtePredict | 14.706 | 0.120 | 14.844 | |
| birteRun | 14.640 | 0.170 | 14.824 | |
| estimateNetwork | 0.001 | 0.000 | 0.001 | |
| getPotentialSwaps | 0.897 | 0.036 | 0.932 | |
| limmaAnalysis | 0.001 | 0.000 | 0.001 | |
| plotConvergence | 0.000 | 0.000 | 0.001 | |
| proposeInteractions | 0.344 | 0.003 | 0.347 | |
| simplify | 0.192 | 0.003 | 0.196 | |
| simulateData | 13.700 | 0.092 | 13.805 | |
| suggestThreshold | 0.517 | 0.004 | 0.521 | |