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###
### Running command:
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###   rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=immunoClust.buildbin-libdir immunoClust_1.28.0.tar.gz
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* installing *source* package 'immunoClust' ...
** using staged installation

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


** libs
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_meta.cpp -o R_meta.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_model.cpp -o R_model.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dist_mvn.cpp -o dist_mvn.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  412 |         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]
  697 |         double maxLike = 0.0;
      |                ^~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  237 |         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]
  523 |         double maxLike = 0.0;
      |                ^~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c em_meta_kl.cpp -o em_meta_kl.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c em_mvn.cpp -o em_mvn.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c em_mvt.cpp -o em_mvt.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c em_mvt2.cpp -o em_mvt2.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hc_meta.cpp -o hc_meta.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hc_mvn.cpp -o hc_mvn.o
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c immunoClust.c -o immunoClust.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c meta_norm.cpp -o meta_norm.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c meta_scale.cpp -o meta_scale.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
  272 |     if( L < COEFF )
      |     ^~
normalize.cpp:275:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  275 |  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]
  377 |     if( L < COEFF )
      |     ^~
normalize.cpp:380:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  380 |  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]
  458 |     if( L < COEFF )
      |     ^~
normalize.cpp:461:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  461 |  int k, j, p;
      |  ^~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sub_mvn.cpp -o sub_mvn.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c util.cpp -o util.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vs_htrans.cpp -o vs_htrans.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/meat/immunoClust.buildbin-libdir/00LOCK-immunoClust/00new/immunoClust/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'immunoClust' as immunoClust_1.28.0.zip
* DONE (immunoClust)