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This page was generated on 2016-08-19 02:39:11 -0700 (Fri, 19 Aug 2016).
| Package 127/1245 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| birte 1.9.2 Holger Froehlich
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] |  | |||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | | |||||
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
| Package: birte |
| Version: 1.9.2 |
| Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings birte_1.9.2.tar.gz |
| StartedAt: 2016-08-18 03:34:58 -0700 (Thu, 18 Aug 2016) |
| EndedAt: 2016-08-18 03:36:32 -0700 (Thu, 18 Aug 2016) |
| EllapsedTime: 94.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: birte.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings birte_1.9.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/birte.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘birte/DESCRIPTION’ ... OK
* this is package ‘birte’ version ‘1.9.2’
* 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
SigGenes: no visible global function definition for ‘toeplitz’
beta.EM: no visible global function definition for ‘hist’
beta.EM: no visible global function definition for ‘lines’
beta.EM: no visible global function definition for ‘dbeta’
birte.aux: no visible global function definition for ‘is’
birte.aux: no visible global function definition for ‘median’
birteFitRidge: no visible global function definition for ‘lm’
birtePredict: no visible binding for global variable ‘sd’
birtePredict: no visible global function definition for ‘predict’
birtePredict: no visible global function definition for ‘coef’
birteRun: no visible global function definition for ‘is’
birteStart: no visible global function definition for ‘head’
birteStart: no visible global function definition for ‘is’
bmixture.mle: no visible global function definition for ‘optim’
dmixture: no visible global function definition for ‘dbeta’
getComponent: no visible global function definition for ‘dbeta’
limmaAnalysis: no visible global function definition for ‘model.matrix’
plotConvergence: no visible global function definition for ‘plot’
plotConvergence: no visible global function definition for ‘abline’
pmixture: no visible global function definition for ‘pbeta’
proposeInteractions: no visible global function definition for ‘dist’
rmix: no visible global function definition for ‘runif’
sample.mRNAData: no visible global function definition for ‘head’
simplify : join.regulators: no visible global function definition for
‘dist’
simplify : join.regulators: no visible global function definition for
‘hclust’
simplify : join.regulators: no visible global function definition for
‘plot’
simplify : join.regulators: no visible global function definition for
‘cutree’
simulateData: no visible global function definition for ‘rbinom’
suggestThreshold: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
abline coef cutree dbeta dist hclust head hist is lines lm median
model.matrix optim pbeta plot predict qbeta rbinom runif sd toeplitz
Consider adding
importFrom("graphics", "abline", "hist", "lines", "plot")
importFrom("methods", "is")
importFrom("stats", "coef", "cutree", "dbeta", "dist", "hclust", "lm",
"median", "model.matrix", "optim", "pbeta", "predict",
"qbeta", "rbinom", "runif", "sd", "toeplitz")
importFrom("utils", "head")
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 ‘_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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
birteFitRidge 6.852 0.096 6.992
birteRun 6.400 0.064 6.476
birtePredict 6.288 0.028 6.330
simulateData 5.952 0.016 5.967
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/birte.Rcheck/00check.log’
for details.
birte.Rcheck/00install.out:
* installing *source* package ‘birte’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
/**
^
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::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)’:
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: In destructor ‘virtual BayesNetwork::˜BayesNetwork()’:
BayesNetwork.cpp:221:8: warning: unused variable ‘i’ [-Wunused-variable]
int c,i,j;
^
BayesNetwork.cpp:221:10: warning: unused variable ‘j’ [-Wunused-variable]
int c,i,j;
^
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::__cxx11::list<int>*, double**, int)’:
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: In member function ‘virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)’:
BayesNetwork.cpp:383:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(p.first == switchid & p.second == mir){
^
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: In member function ‘virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)’:
BayesNetwork.cpp:599:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(add != R[c].n_cols){
^
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::swap_states(int**, int, int, std::set<int>*, std::__cxx11::list<int>*, std::set<int>**, double)’:
BayesNetwork.cpp:669:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(swapid1 >= swap_idx[condition].size()) {
^
BayesNetwork.cpp:665:6: warning: unused variable ‘pos_swaps’ [-Wunused-variable]
int pos_swaps = 0, condition, condition1, condition2, counter;
^
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::MCMC(long int, long int, int, double*)’:
BayesNetwork.cpp:842:6: warning: unused variable ‘mir’ [-Wunused-variable]
int mir, tf;
^
BayesNetwork.cpp:842:11: warning: unused variable ‘tf’ [-Wunused-variable]
int mir, tf;
^
BayesNetwork.cpp:847:7: warning: unused variable ‘eff_samples’ [-Wunused-variable]
long eff_samples = niter / thin + 1;
^
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: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:910:102: 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: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: In member function ‘virtual double BayesNetwork::likelihood()’:
BayesNetwork.cpp:1074:12: warning: unused variable ‘j’ [-Wunused-variable]
int c, i, j, r;
^
BayesNetwork.cpp:1075:9: warning: unused variable ‘bn’ [-Wunused-variable]
double bn;
^
BayesNetwork.cpp:1078:9: warning: unused variable ‘z’ [-Wunused-variable]
double z;
^
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::MCMC(long int, long int, int, double*)’:
BayesNetwork.cpp:1026:26: warning: ‘delta_loglik’ may be used uninitialized in this function [-Wmaybe-uninitialized]
log_lik += delta_loglik;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
/**
^
getStates.cpp: In function ‘SEXPREC* getStates(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
getStates.cpp:349:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(S2O == NULL | SparentsOfO == NULL)
^
getStates.cpp:366:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(T2O == NULL | TparentsOfO == NULL)
^
getStates.cpp:384:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(Q2O == NULL | QparentsOfO == NULL)
^
Loading required package: Rcpp
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.4-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 | 6.852 | 0.096 | 6.992 | |
| birtePredict | 6.288 | 0.028 | 6.330 | |
| birteRun | 6.400 | 0.064 | 6.476 | |
| estimateNetwork | 0 | 0 | 0 | |
| getPotentialSwaps | 0.440 | 0.012 | 0.450 | |
| limmaAnalysis | 0.000 | 0.000 | 0.001 | |
| plotConvergence | 0.000 | 0.000 | 0.001 | |
| proposeInteractions | 0.184 | 0.004 | 0.184 | |
| simplify | 0.100 | 0.012 | 0.114 | |
| simulateData | 5.952 | 0.016 | 5.967 | |
| suggestThreshold | 0.524 | 0.000 | 0.527 | |