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BUILD BIN report for immunoClust on tokay1

This page was generated on 2019-04-13 11:25:00 -0400 (Sat, 13 Apr 2019).

Package 770/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunoClust 1.14.1
Till Soerensen
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/immunoClust
Branch: RELEASE_3_8
Last Commit: c89a3c8
Last Changed Date: 2018-12-01 05:45:45 -0400 (Sat, 01 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: immunoClust
Version: 1.14.1
Command: rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.14.1.tar.gz
StartedAt: 2019-04-13 07:31:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 07:32:33 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 47.9 seconds
RetCode: 0
Status:  OK  
PackageFile: immunoClust_1.14.1.zip
PackageFileSize: 4.088 MiB

Command output

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###
### Running command:
###
###   rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.14.1.tar.gz
###
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install for i386

* installing *source* package 'immunoClust' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_meta.cpp -o R_meta.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_model.cpp -o R_model.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function 'int dist_mvn::hellinger(double*)':
dist_mvn.cpp:56:14: warning: variable 'det_k' set but not used [-Wunused-but-set-variable]
  double det, det_k, det_l, logD;
              ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::bt_step()':
em_meta.cpp:704:10: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
   double sndLike = 0.0;
          ^
em_meta.cpp: In member function 'int em_meta::wt_step()':
em_meta.cpp:1047:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1049:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
em_meta.cpp: In member function 'int em_meta::st_step()':
em_meta.cpp:1117:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1119:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvn.cpp -o em_mvn.o
em_mvn.cpp: In member function 'int em_gaussian::build(const int*, double*, int*)':
em_mvn.cpp:721:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function 'int em_mvt::t_step()':
em_mvt.cpp:521:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt.cpp: In member function 'int em_mvt::build(const int*, double*, int*)':
em_mvt.cpp:771:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt2.cpp -o em_mvt2.o
em_mvt2.cpp: In member function 'int em_mvt2::t_step()':
em_mvt2.cpp:508:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt2.cpp: In member function 'int em_mvt2::build(const int*, double*, int*)':
em_mvt2.cpp:805:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function 'int mvn_dendro::mahalanobis_w(int*, int*, double*)':
hc_meta.cpp:814:16: warning: variable 'S_i' set but not used [-Wunused-but-set-variable]
  const double *S_i, *S_j;
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_mvn.cpp -o hc_mvn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c immunoClust.c -o immunoClust.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_norm.cpp -o meta_norm.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function 'void meta_scale::quantile()':
meta_scale.cpp:846:10: warning: variable 'w' set but not used [-Wunused-but-set-variable]
  double *w, *m, *s;
          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c normalize.cpp -o normalize.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sub_mvn.cpp -o sub_mvn.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c util.cpp -o util.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vs_htrans.cpp -o vs_htrans.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/i386/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'immunoClust'
    finding HTML links ... done
    cell.ClustData                          html  
    cell.EM                                 html  
    cell.FitModel                           html  
    cell.ME                                 html  
    cell.SubClustering                      html  
    cell.hclust                             html  
    cell.process                            html  
    cell.removed                            html  
    dat.exp                                 html  
    dat.fcs                                 html  
    dat.meta                                html  
    immunoClust-package                     html  
    immunoClust.object                      html  
    meta.ME                                 html  
    meta.SubClustering                      html  
    meta.clustering                         html  
    meta.export                             html  
    meta.exprs                              html  
    meta.hclust                             html  
    meta.normalize                          html  
    meta.plot                               html  
    meta.process                            html  
    meta.regnorm                            html  
    plot.immunoClust                        html  
    splom.immunoClust                       html  
    trans.ApplyToData                       html  
    trans.FitToData                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'immunoClust' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_meta.cpp -o R_meta.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_model.cpp -o R_model.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dist_mvn.cpp -o dist_mvn.o
dist_mvn.cpp: In member function 'int dist_mvn::hellinger(double*)':
dist_mvn.cpp:56:14: warning: variable 'det_k' set but not used [-Wunused-but-set-variable]
  double det, det_k, det_l, logD;
              ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::bt_step()':
em_meta.cpp:704:10: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
   double sndLike = 0.0;
          ^
em_meta.cpp: In member function 'int em_meta::wt_step()':
em_meta.cpp:1047:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1049:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
em_meta.cpp: In member function 'int em_meta::st_step()':
em_meta.cpp:1117:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_meta.cpp:1119:9: warning: variable 'minDelta' set but not used [-Wunused-but-set-variable]
  double minDelta = FLTMAX;
         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvn.cpp -o em_mvn.o
em_mvn.cpp: In member function 'int em_gaussian::build(const int*, double*, int*)':
em_mvn.cpp:721:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt.cpp -o em_mvt.o
em_mvt.cpp: In member function 'int em_mvt::t_step()':
em_mvt.cpp:521:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt.cpp: In member function 'int em_mvt::build(const int*, double*, int*)':
em_mvt.cpp:771:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em_mvt2.cpp -o em_mvt2.o
em_mvt2.cpp: In member function 'int em_mvt2::t_step()':
em_mvt2.cpp:508:9: warning: variable 'minNk' set but not used [-Wunused-but-set-variable]
  double minNk = T_sum;
         ^
em_mvt2.cpp: In member function 'int em_mvt2::build(const int*, double*, int*)':
em_mvt2.cpp:805:13: warning: variable 'maxClust' set but not used [-Wunused-but-set-variable]
         int maxClust = -1;
             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_meta.cpp -o hc_meta.o
hc_meta.cpp: In member function 'int mvn_dendro::mahalanobis_w(int*, int*, double*)':
hc_meta.cpp:814:16: warning: variable 'S_i' set but not used [-Wunused-but-set-variable]
  const double *S_i, *S_j;
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hc_mvn.cpp -o hc_mvn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c immunoClust.c -o immunoClust.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_norm.cpp -o meta_norm.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c meta_scale.cpp -o meta_scale.o
meta_scale.cpp: In member function 'void meta_scale::quantile()':
meta_scale.cpp:846:10: warning: variable 'w' set but not used [-Wunused-but-set-variable]
  double *w, *m, *s;
          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c normalize.cpp -o normalize.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sub_mvn.cpp -o sub_mvn.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c util.cpp -o util.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vs_htrans.cpp -o vs_htrans.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_mvn.o em_mvt.o em_mvt2.o hc_meta.o hc_mvn.o immunoClust.o meta_norm.o meta_scale.o normalize.o sub_mvn.o util.o vs_htrans.o -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'immunoClust' as immunoClust_1.14.1.zip
* DONE (immunoClust)
In R CMD INSTALL
In R CMD INSTALL