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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FunChIP_1.20.0.tar.gz && rm -rf FunChIP.buildbin-libdir && mkdir FunChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FunChIP.buildbin-libdir FunChIP_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FunChIP_1.20.0.zip && rm FunChIP_1.20.0.tar.gz FunChIP_1.20.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2 22.0M    2  508k    0     0   715k      0  0:00:31 --:--:--  0:00:31  715k
  8 22.0M    8 2011k    0     0  1175k      0  0:00:19  0:00:01  0:00:18 1175k
 19 22.0M   19 4362k    0     0  1618k      0  0:00:13  0:00:02  0:00:11 1618k
 34 22.0M   34 7716k    0     0  2088k      0  0:00:10  0:00:03  0:00:07 2088k
 52 22.0M   52 11.5M    0     0  2518k      0  0:00:08  0:00:04  0:00:04 2518k
 75 22.0M   75 16.6M    0     0  2982k      0  0:00:07  0:00:05  0:00:02 3305k
100 22.0M  100 22.0M    0     0  3418k      0  0:00:06  0:00:06 --:--:-- 4203k

install for i386

* installing *source* package 'FunChIP' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -I. -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmean_function.cpp -o kmean_function.o
kmean_function.cpp: In function 'SEXPREC* kmean_function(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:74:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for (unsigned int i =0 ; i<num_data; i++){
                              ~^~~~~~~~~
kmean_function.cpp:80:34: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       for (unsigned int t =0 ; t < num_points; t++)
                                ~~^~~~~~~~~~~~
kmean_function.cpp: In function 'SEXPREC* distance_matrix(SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:210:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
         for (unsigned int i =0 ; i<num_data; i++){
                                  ~^~~~~~~~~
kmean_function.cpp:216:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
             for (unsigned int t =0 ; t < num_points; t++)
                                      ~~^~~~~~~~~~~~
kmean_function.cpp: In function 'void kma_discrete(std::vector<peak>&, const int&, std::vector<int>&, const double&, const double&, const int&, const char&, const double&, const double&, std::vector<int>&, std::vector<double>&, std::vector<int>&, const double&, const double&, int, char, char)':
kmean_function.cpp:638:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   while( iter < iter_max and number_distances_low < dati.size()  and cluster_vuoti==0){  //and number_clusters_different > 0
                              ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
kmean_function.cpp:677:52: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
       if ( (unsigned int)number_clusters_different == dati.size() & iter != 1)
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
kmean_function.cpp:681:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if (number_distances_low== dati.size())
           ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
kmean_function.cpp: In function 'void normalize_data(std::vector<int>&, std::vector<int>&, const int&)':
kmean_function.cpp:759:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
   for (unsigned int i=0; i<n_clust; i++)
                          ~^~~~~~~~
In file included from kmean_function.cpp:1:
peak.h: In member function 'std::vector<double> peak::area(int, char) const':
peak.h:154:46: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 area_def[0] = sqrt(area[0]/2)/D;
                               ~~~~~~~~~~~~~~~^~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o FunChIP.dll tmp.def kmean_function.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FunChIP.buildbin-libdir/00LOCK-FunChIP/00new/FunChIP/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FunChIP'
    finding HTML links ... done
    FunChIP-package                         html  
    GR100                                   html  
    finding level-2 HTML links ... done

    bending_index                           html  
    choose_k-method                         html  
    cluster_peak-method                     html  
    compute_fragments_length                html  
    distance_peak                           html  
    peaks                                   html  
    pileup_peak-method                      html  
    plot_peak-method                        html  
    silhouette_plot                         html  
    smooth_peak-method                      html  
    summit_peak-method                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'FunChIP' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -I. -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmean_function.cpp -o kmean_function.o
kmean_function.cpp: In function 'SEXPREC* kmean_function(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:74:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for (unsigned int i =0 ; i<num_data; i++){
                              ~^~~~~~~~~
kmean_function.cpp:80:34: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       for (unsigned int t =0 ; t < num_points; t++)
                                ~~^~~~~~~~~~~~
kmean_function.cpp: In function 'SEXPREC* distance_matrix(SEXP, SEXP, SEXP, SEXP, SEXP)':
kmean_function.cpp:210:35: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
         for (unsigned int i =0 ; i<num_data; i++){
                                  ~^~~~~~~~~
kmean_function.cpp:216:40: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
             for (unsigned int t =0 ; t < num_points; t++)
                                      ~~^~~~~~~~~~~~
kmean_function.cpp: In function 'void kma_discrete(std::vector<peak>&, const int&, std::vector<int>&, const double&, const double&, const int&, const char&, const double&, const double&, std::vector<int>&, std::vector<double>&, std::vector<int>&, const double&, const double&, int, char, char)':
kmean_function.cpp:638:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   while( iter < iter_max and number_distances_low < dati.size()  and cluster_vuoti==0){  //and number_clusters_different > 0
                              ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
kmean_function.cpp:677:52: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
       if ( (unsigned int)number_clusters_different == dati.size() & iter != 1)
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
kmean_function.cpp:681:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<peak>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       if (number_distances_low== dati.size())
           ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
kmean_function.cpp: In function 'void normalize_data(std::vector<int>&, std::vector<int>&, const int&)':
kmean_function.cpp:759:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare]
   for (unsigned int i=0; i<n_clust; i++)
                          ~^~~~~~~~
In file included from kmean_function.cpp:1:
peak.h: In member function 'std::vector<double> peak::area(int, char) const':
peak.h:154:46: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 area_def[0] = sqrt(area[0]/2)/D;
                               ~~~~~~~~~~~~~~~^~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FunChIP.dll tmp.def kmean_function.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FunChIP.buildbin-libdir/FunChIP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FunChIP' as FunChIP_1.20.0.zip
* DONE (FunChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'FunChIP' successfully unpacked and MD5 sums checked