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BioC 3.4: CHECK report for networkBMA on malbec1

This page was generated on 2017-04-15 16:11:01 -0400 (Sat, 15 Apr 2017).

Package 841/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.12.0
Ka Yee Yeung
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/networkBMA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: networkBMA
Version: 2.12.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings networkBMA_2.12.0.tar.gz
StartedAt: 2017-04-15 00:08:55 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:10:35 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 99.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: networkBMA.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings networkBMA_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘networkBMA/DESCRIPTION’ ... OK
* this is package ‘networkBMA’ version ‘2.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  bmaNoMPI.hpp config.h.in fastBMA.hpp my_sort.hpp
These are unlikely file names for src files.
* 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 ‘networkBMA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘RcppArmadillo::fastLmPure’ by ‘RcppEigen::fastLmPure’ when loading ‘networkBMA’
  Warning: replacing previous import ‘RcppArmadillo::fastLm’ by ‘RcppEigen::fastLm’ when loading ‘networkBMA’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.1Mb
* 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
bicreg.pr: no visible global function definition for ‘leaps’
bicreg.pr.resid: no visible global function definition for ‘leaps’
Undefined global functions or variables:
  leaps
* 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 ... WARNING
File ‘networkBMA/libs/networkBMA.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
    Object: ‘ScanBMA_full.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck/00check.log’
for details.

networkBMA.Rcheck/00install.out:

* installing *source* package ‘networkBMA’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I./include -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2 -c MurmurHash3.cpp -o MurmurHash3.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I./include -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I./include -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2 -c ScanBMA_full.cpp -o ScanBMA_full.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from ScanBMA_full.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
ScanBMA_full.cpp: In function ‘const List ScanBMA_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double)’:
ScanBMA_full.cpp:132:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:462:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:323:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:462:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List ScanBMA_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, double)’:
ScanBMA_full.cpp:416:45: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:462:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
ScanBMA_full.cpp: In function ‘const List BMA_Diff_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, Rcpp::IntegerVector, bool, bool, Rcpp::IntegerVector, Rcpp::IntegerVector, double, double)’:
ScanBMA_full.cpp:609:43: warning: ‘const arma::mtOp<unsigned int, T1, arma::op_sort_index> arma::sort_index(const arma::Base<typename T1::elem_type, T1>&, arma::uword) [with T1 = arma::Mat<double>; typename T1::elem_type = double; arma::uword = unsigned int]’ is deprecated [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo:462:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43:1: note: declared here
 sort_index
 ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I./include -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/BH/include"   -fpic  -g -O2 -c fastBMAR.cpp -o fastBMAR.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o networkBMA.so MurmurHash3.o RcppExports.o ScanBMA_full.o fastBMAR.o -llapack -lblas -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/networkBMA.Rcheck/networkBMA/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘RcppArmadillo::fastLmPure’ by ‘RcppEigen::fastLmPure’ when loading ‘networkBMA’
Warning: replacing previous import ‘RcppArmadillo::fastLm’ by ‘RcppEigen::fastLm’ when loading ‘networkBMA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘RcppArmadillo::fastLmPure’ by ‘RcppEigen::fastLmPure’ when loading ‘networkBMA’
Warning: replacing previous import ‘RcppArmadillo::fastLm’ by ‘RcppEigen::fastLm’ when loading ‘networkBMA’
* DONE (networkBMA)

networkBMA.Rcheck/networkBMA-Ex.timings:

nameusersystemelapsed
ScanBMA0.1240.0000.124
ScanBMAcontrol4.7000.0044.709
contabs1.3640.0121.379
contabs.netwBMA0.0000.0000.001
contabs.prelim0.0000.0000.001
fastBMAcontrol0.0640.0040.081
fastgControl0.0680.0000.067
gControl4.3720.0084.382
iBMAcontrolLM0.5040.0040.510
iterateBMAlm0.7640.0040.770
networkBMA0.2600.0080.271
roc0.6640.0000.665
scores0.6880.0040.693
summary.networkBMA0.2640.0040.268
varord0.1680.0040.171
vignette3.6480.0043.651
writeEdges0.5600.0040.565