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BioC 3.3: CHECK report for birte on zin2

This page was generated on 2016-10-13 12:45:23 -0700 (Thu, 13 Oct 2016).

Package 123/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.8.1
Holger Froehlich
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/birte
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: birte
Version: 1.8.1
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings birte_1.8.1.tar.gz
StartedAt: 2016-10-12 23:57:53 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:59:37 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 103.5 seconds
RetCode: 0
Status:  OK 
CheckDir: birte.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings birte_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.8.1’
* 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 ‘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’
birteStart: no visible global function definition for ‘head’
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 lines lm median
  model.matrix optim pbeta plot predict qbeta rbinom runif sd toeplitz
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "plot")
  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.
* 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 7.864  0.047   7.937
birteRun      7.137  0.020   7.266
birtePredict  6.947  0.024   6.978
simulateData  6.752  0.056   6.860
* 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-3.3-bioc/meat/birte.Rcheck/00check.log’
for details.

birte.Rcheck/00install.out:

* installing *source* package ‘birte’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-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::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int>*, std::list<int>*, std::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::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:599:19: 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::list<int>*, std::set<int>**, double)’:
BayesNetwork.cpp:669:42: 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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.3-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
birteFitRidge7.8640.0477.937
birtePredict6.9470.0246.978
birteRun7.1370.0207.266
estimateNetwork000
getPotentialSwaps0.4260.0040.430
limmaAnalysis000
plotConvergence000
proposeInteractions0.2330.0040.238
simplify0.1550.0040.158
simulateData6.7520.0566.860
suggestThreshold0.4310.0080.448