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INSTALL report for networkBMA on tokay2

This page was generated on 2019-04-09 12:00:54 -0400 (Tue, 09 Apr 2019).

Package 1082/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
networkBMA 2.23.0
Ka Yee Yeung
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/networkBMA
Branch: master
Last Commit: 06406b4
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ ERROR ] ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: networkBMA
Version: 2.23.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/networkBMA_2.23.0.tar.gz && rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=networkBMA.buildbin-libdir networkBMA_2.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL networkBMA_2.23.0.zip && rm networkBMA_2.23.0.tar.gz networkBMA_2.23.0.zip
StartedAt: 2019-04-08 19:02:41 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 19:04:32 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 111.1 seconds
RetCode: 1
Status:  ERROR  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/networkBMA_2.23.0.tar.gz && rm -rf networkBMA.buildbin-libdir && mkdir networkBMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=networkBMA.buildbin-libdir networkBMA_2.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL networkBMA_2.23.0.zip && rm networkBMA_2.23.0.tar.gz networkBMA_2.23.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 1318k  100 1318k    0     0  17.1M      0 --:--:-- --:--:-- --:--:-- 18.9M

install for i386

* installing *source* package 'networkBMA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c MurmurHash3.cpp -o MurmurHash3.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DWIN=1 -DUSE_RBLAS -I./include -I.  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=generic -c ScanBMA_full.cpp -o ScanBMA_full.o
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/unordered_set:35:0,
                 from ScanBMA_full.cpp:18:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
ScanBMA_full.cpp: In function 'const List ScanBMA_BIC(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double)':
ScanBMA_full.cpp:137:45: 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 (declared at C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
ScanBMA_full.cpp:19:28: error: 'unordered_set' is not a member of 'std'
 #define UNORDERED_SET_TYPE std::unordered_set
                            ^
ScanBMA_full.cpp:161:3: note: in expansion of macro 'UNORDERED_SET_TYPE'
   UNORDERED_SET_TYPE<std::string> checkedModels;
   ^
ScanBMA_full.cpp:19:28: note: suggested alternative:
 #define UNORDERED_SET_TYPE std::unordered_set
                            ^
ScanBMA_full.cpp:161:3: note: in expansion of macro 'UNORDERED_SET_TYPE'
   UNORDERED_SET_TYPE<std::string> checkedModels;
   ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_set:42:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:181,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:59,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_set.h:173:11: note:   'std::tr1::unordered_set'
     class unordered_set
           ^
ScanBMA_full.cpp:161:33: error: expected primary-expression before '>' token
   UNORDERED_SET_TYPE<std::string> checkedModels;
                                 ^
ScanBMA_full.cpp:161:35: error: 'checkedModels' was not declared in this scope
   UNORDERED_SET_TYPE<std::string> checkedModels;
                                   ^
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:328:43: 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 (declared at C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
ScanBMA_full.cpp: In function 'const List ScanBMA_g(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericVector, double, double)':
ScanBMA_full.cpp:421:45: 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 (declared at C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
   arma::uvec pord = sort_index(priorProbs, 1);
                                             ^
ScanBMA_full.cpp:19:28: error: 'unordered_set' is not a member of 'std'
 #define UNORDERED_SET_TYPE std::unordered_set
                            ^
ScanBMA_full.cpp:445:3: note: in expansion of macro 'UNORDERED_SET_TYPE'
   UNORDERED_SET_TYPE<std::string> checkedModels;
   ^
ScanBMA_full.cpp:19:28: note: suggested alternative:
 #define UNORDERED_SET_TYPE std::unordered_set
                            ^
ScanBMA_full.cpp:445:3: note: in expansion of macro 'UNORDERED_SET_TYPE'
   UNORDERED_SET_TYPE<std::string> checkedModels;
   ^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_set:42:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:181,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:59,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:26,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from ScanBMA_full.cpp:5:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_set.h:173:11: note:   'std::tr1::unordered_set'
     class unordered_set
           ^
ScanBMA_full.cpp:445:33: error: expected primary-expression before '>' token
   UNORDERED_SET_TYPE<std::string> checkedModels;
                                 ^
ScanBMA_full.cpp:445:35: error: 'checkedModels' was not declared in this scope
   UNORDERED_SET_TYPE<std::string> checkedModels;
                                   ^
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:614:43: 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 (declared at C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/fn_sort_index.hpp:43) [-Wdeprecated-declarations]
 arma::uvec pord = sort_index(priorProbs, 1);
                                           ^
make: *** [ScanBMA_full.o] Error 1
ERROR: compilation failed for package 'networkBMA'
* removing 'C:/Users/biocbuild/bbs-3.9-bioc/meat/networkBMA.buildbin-libdir/networkBMA'