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BUILD BIN report for immunoClust on tokay1

This page was generated on 2021-05-06 12:31:49 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the immunoClust package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 887/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
immunoClust 1.22.0  (landing page)
Till Soerensen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/immunoClust
Branch: RELEASE_3_12
Last Commit: f078aa9
Last Changed Date: 2020-10-27 11:03:10 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: immunoClust
Version: 1.22.0
Command: rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.22.0.tar.gz
StartedAt: 2021-05-06 09:19:45 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 09:20:30 -0400 (Thu, 06 May 2021)
EllapsedTime: 45.3 seconds
RetCode: 0
Status:   OK   
PackageFile: immunoClust_1.22.0.zip
PackageFileSize: 5.01 MiB

Command output

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###
### Running command:
###
###   rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.22.0.tar.gz
###
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install for i386

* installing *source* package 'immunoClust' ...
** using staged installation

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


** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_meta.cpp -o R_meta.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_model.cpp -o R_model.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c dist_mvn.cpp -o dist_mvn.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::et_step()':
em_meta.cpp:412:16: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
         double sndLike = 0.0;
                ^~~~~~~
em_meta.cpp: In member function 'double em_meta::fixedN_et_step()':
em_meta.cpp:697:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
         double maxLike = 0.0;
                ^~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_meta_bc.cpp -o em_meta_bc.o
em_meta_bc.cpp: In member function 'double em_meta::bc_et_step()':
em_meta_bc.cpp:237:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
         double maxLike = 0.0;
                ^~~~~~~
em_meta_bc.cpp: In member function 'double em_meta::bc_fixedN_et_step()':
em_meta_bc.cpp:523:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
         double maxLike = 0.0;
                ^~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_meta_kl.cpp -o em_meta_kl.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_mvn.cpp -o em_mvn.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_mvt.cpp -o em_mvt.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_mvt2.cpp -o em_mvt2.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hc_meta.cpp -o hc_meta.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hc_mvn.cpp -o hc_mvn.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c immunoClust.c -o immunoClust.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c meta_norm.cpp -o meta_norm.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c meta_scale.cpp -o meta_scale.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c normalize.cpp -o normalize.o
normalize.cpp: In member function 'int normalize::scale_X(int, int)':
normalize.cpp:272:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:275:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  int k, j, p;
  ^~~
normalize.cpp: In member function 'int normalize::linear_Y(int, int)':
normalize.cpp:377:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:380:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  int k, j, p;
  ^~~
normalize.cpp: In member function 'int normalize::scale_Y(int, int)':
normalize.cpp:458:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:461:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  int k, j, p;
  ^~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c sub_mvn.cpp -o sub_mvn.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c vs_htrans.cpp -o vs_htrans.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_meta_bc.o em_meta_kl.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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/immunoClust.buildbin-libdir/00LOCK-immunoClust/00new/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
    bhattacharyya                           html  
    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  
    generics                                html  
    immunoClust-package                     html  
    immunoClust.methods                     html  
    immunoClust.object                      html  
    immunoMeta.methods                      html  
    immunoMeta.object                       html  
    meta.ME                                 html  
    meta.SubClustering                      html  
    meta.clustering                         html  
    meta.export                             html  
    meta.exprs                              html  
    meta.hclust                             html  
    meta.normalize                          html  
    meta.process                            html  
    meta.regnorm                            html  
    plot.immunoClust                        html  
    plot.immunoMeta                         html  
    splom.immunoClust                       html  
    trans.ApplyToData                       html  
    trans.FitToData                         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 'immunoClust' ...

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


** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_meta.cpp -o R_meta.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_model.cpp -o R_model.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c dist_mvn.cpp -o dist_mvn.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_meta.cpp -o em_meta.o
em_meta.cpp: In member function 'double em_meta::et_step()':
em_meta.cpp:412:16: warning: variable 'sndLike' set but not used [-Wunused-but-set-variable]
         double sndLike = 0.0;
                ^~~~~~~
em_meta.cpp: In member function 'double em_meta::fixedN_et_step()':
em_meta.cpp:697:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
         double maxLike = 0.0;
                ^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_meta_bc.cpp -o em_meta_bc.o
em_meta_bc.cpp: In member function 'double em_meta::bc_et_step()':
em_meta_bc.cpp:237:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
         double maxLike = 0.0;
                ^~~~~~~
em_meta_bc.cpp: In member function 'double em_meta::bc_fixedN_et_step()':
em_meta_bc.cpp:523:16: warning: variable 'maxLike' set but not used [-Wunused-but-set-variable]
         double maxLike = 0.0;
                ^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_meta_kl.cpp -o em_meta_kl.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_mvn.cpp -o em_mvn.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_mvt.cpp -o em_mvt.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c em_mvt2.cpp -o em_mvt2.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hc_meta.cpp -o hc_meta.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c hc_mvn.cpp -o hc_mvn.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c immunoClust.c -o immunoClust.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c meta_norm.cpp -o meta_norm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c meta_scale.cpp -o meta_scale.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c normalize.cpp -o normalize.o
normalize.cpp: In member function 'int normalize::scale_X(int, int)':
normalize.cpp:272:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:275:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  int k, j, p;
  ^~~
normalize.cpp: In member function 'int normalize::linear_Y(int, int)':
normalize.cpp:377:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:380:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  int k, j, p;
  ^~~
normalize.cpp: In member function 'int normalize::scale_Y(int, int)':
normalize.cpp:458:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:461:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  int k, j, p;
  ^~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c sub_mvn.cpp -o sub_mvn.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c vs_htrans.cpp -o vs_htrans.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o immunoClust.dll tmp.def R_meta.o R_model.o dist_mvn.o em_meta.o em_meta_bc.o em_meta_kl.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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'immunoClust' as immunoClust_1.22.0.zip
* DONE (immunoClust)