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This page was generated on 2017-08-16 13:32:53 -0400 (Wed, 16 Aug 2017).
| Package 141/1382 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| birte 1.12.0 Holger Froehlich
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | |||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: birte |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings birte_1.12.0.tar.gz |
| StartedAt: 2017-08-16 00:20:58 -0400 (Wed, 16 Aug 2017) |
| EndedAt: 2017-08-16 00:23:03 -0400 (Wed, 16 Aug 2017) |
| EllapsedTime: 126.0 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/birte.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘birte/DESCRIPTION’ ... OK
* this is package ‘birte’ version ‘1.12.0’
* 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 ... 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
birte.aux: no visible global function definition for ‘is’
birteRun: no visible global function definition for ‘is’
birteStart: no visible global function definition for ‘is’
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
birteFitRidge 7.510 0.118 7.779
birtePredict 7.341 0.080 7.633
birteRun 6.043 0.075 6.251
simulateData 5.387 0.053 5.556
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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:96:8: warning: unused variable 'j' [-Wunused-variable]
int i,j,c,r;
^
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-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:357:6: warning: unused variable 'found' [-Wunused-variable]
int found, omega_index = 0, i, j;
^
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-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:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^
BayesNetwork.cpp: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:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^
BayesNetwork.cpp: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: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: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: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:842:11: warning: unused variable 'tf' [-Wunused-variable]
int mir, tf;
^
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
int mir, tf;
^
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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -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-3.5-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 | 7.510 | 0.118 | 7.779 | |
| birtePredict | 7.341 | 0.080 | 7.633 | |
| birteRun | 6.043 | 0.075 | 6.251 | |
| estimateNetwork | 0.001 | 0.000 | 0.000 | |
| getPotentialSwaps | 0.407 | 0.013 | 0.436 | |
| limmaAnalysis | 0.000 | 0.000 | 0.001 | |
| plotConvergence | 0.000 | 0.000 | 0.001 | |
| proposeInteractions | 0.334 | 0.006 | 0.352 | |
| simplify | 0.159 | 0.002 | 0.168 | |
| simulateData | 5.387 | 0.053 | 5.556 | |
| suggestThreshold | 0.284 | 0.003 | 0.311 | |