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BioC 3.1: CHECK report for birte on morelia

This page was generated on 2015-10-09 09:42:39 -0700 (Fri, 09 Oct 2015).

Package 109/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.2.0
Holger Froehlich
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/birte
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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 23:41:24 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:42:59 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 94.9 seconds
RetCode: 0
Status:  OK 
CheckDir: birte.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings birte_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/birte.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [16s/16s] 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 ‘__ZNSt3__14coutE’, 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 ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
birteRun      7.542  0.337   7.891
birteFitRidge 7.565  0.301   7.869
birtePredict  7.350  0.405   7.767
simulateData  6.866  0.360   7.229
* 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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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  -Wall -mtune=core2 -g -O2  -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:
./BayesNetwork.h:203:3: warning: '/*' within block comment [-Wcomment]
                /**
                ^
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-Wunused-variable]
        int i,j,c,r;
                  ^
BayesNetwork.cpp:96:8: warning: unused variable 'j' [-Wunused-variable]
        int i,j,c,r;
              ^
BayesNetwork.cpp:221:10: warning: unused variable 'j' [-Wunused-variable]
        int c,i,j;
                ^
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-Wunused-variable]
        int c,i,j;
              ^
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-Wunused-variable]
        int found, omega_index = 0, i, j;
                                    ^
BayesNetwork.cpp:357:6: warning: unused variable 'found' [-Wunused-variable]
        int found, omega_index = 0, i, j;
            ^
BayesNetwork.cpp:380:11: warning: unused variable 'k' [-Wunused-variable]
        int j=1, k, del=-1;      // j startet bei 1, weil die 1. Spalte der Intercept ist
                 ^
BayesNetwork.cpp:665:6: warning: unused variable 'pos_swaps' [-Wunused-variable]
        int pos_swaps = 0, condition, condition1, condition2, counter;
            ^
BayesNetwork.cpp:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                                               ^
BayesNetwork.cpp:909:26: warning: unused variable 'delta_prior' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                ^
BayesNetwork.cpp:909:23: warning: unused variable 'u' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                             ^
BayesNetwork.cpp:842:11: warning: unused variable 'tf' [-Wunused-variable]
        int mir, tf;
                 ^
BayesNetwork.cpp:909:48: warning: unused variable 'eps_old' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                                      ^
BayesNetwork.cpp:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
        double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;        
                                             ^
BayesNetwork.cpp:910:119: warning: unused variable 'cond' [-Wunused-variable]
        int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                                             ^
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
        int mir, tf;
            ^
BayesNetwork.cpp:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
        long eff_samples = niter / thin + 1;
             ^
BayesNetwork.cpp:910:102: warning: unused variable 'make_move_eps' [-Wunused-variable]
        int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                            ^
BayesNetwork.cpp:1074:12: warning: unused variable 'j' [-Wunused-variable]
        int c, i, j, r;
                  ^
BayesNetwork.cpp:1078:9: warning: unused variable 'z' [-Wunused-variable]
        double z;
               ^
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
        double bn; 
               ^
22 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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  -Wall -mtune=core2 -g -O2  -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:
./BayesNetwork.h:203:3: warning: '/*' within block comment [-Wcomment]
                /**
                ^
1 warning generated.
Loading required package: Rcpp
clang++ -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 -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:

nameusersystemelapsed
birteFitRidge7.5650.3017.869
birtePredict7.3500.4057.767
birteRun7.5420.3377.891
estimateNetwork0.0010.0000.000
getPotentialSwaps0.6150.0250.679
limmaAnalysis0.0010.0000.000
plotConvergence0.0010.0000.000
proposeInteractions0.2270.0410.268
simplify0.1240.0160.141
simulateData6.8660.3607.229
suggestThreshold0.3220.0030.325