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CHECK report for birte on malbec2

This page was generated on 2018-10-17 08:27:12 -0400 (Wed, 17 Oct 2018).

Package 155/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.16.0
Holger Froehlich
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/birte
Branch: RELEASE_3_7
Last Commit: c210f9b
Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: birte
Version: 1.16.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:birte.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings birte_1.16.0.tar.gz
StartedAt: 2018-10-15 22:51:05 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:52:18 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 73.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: birte.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:birte.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings birte_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/birte.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
  BayesNetwork.cpp:383:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  getStates.cpp:349:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  getStates.cpp:366:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  getStates.cpp:384:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.7-bioc/meat/birte.Rcheck/00install.out’ for details.
* 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 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
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/birte/libs/birte.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
birteFitRidge 5.616  0.108   6.038
birtePredict  5.300  0.036   5.340
birteRun      4.992  0.044   5.048
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/birte.Rcheck/00check.log’
for details.

Installation output

birte.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL birte
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘birte’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/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]
   /**
   ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from BayesNetwork.h:36,
                 from BayesNetwork.cpp:26:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
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-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/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]
   /**
   ^
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from getStates.cpp:23:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
     #pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
                                                                                                            ^
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-3.7-bioc/R/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.7-bioc/R/library/birte/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (birte)

Tests output

Example timings

birte.Rcheck/birte-Ex.timings

nameusersystemelapsed
birteFitRidge5.6160.1086.038
birtePredict5.3000.0365.340
birteRun4.9920.0445.048
estimateNetwork0.0040.0000.000
getPotentialSwaps0.3440.0160.360
limmaAnalysis000
plotConvergence0.0000.0000.001
proposeInteractions0.1560.0280.185
simplify0.1160.0080.123
simulateData4.2600.0284.293
suggestThreshold0.2880.0000.286