Multiple platform build/check report for BioC 3.9 - INSTALL report for immunoClust on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL immunoClust
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘immunoClust’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c R_meta.cpp -o R_meta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c R_model.cpp -o R_model.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
              ^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
         ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
             ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
             ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
             ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
                ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c hc_mvn.cpp -o hc_mvn.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c immunoClust.c -o immunoClust.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c meta_norm.cpp -o meta_norm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -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;
          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c normalize.cpp -o normalize.o
normalize.cpp: In member function ‘int normalize::linear_X(int, int)’:
normalize.cpp:156:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:159:2: 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_X(int, int)’:
normalize.cpp:271:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:274:2: 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:459:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if( L < COEFF )
     ^~
normalize.cpp:462:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  int k, j, p;
  ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c sub_mvn.cpp -o sub_mvn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c util.cpp -o util.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c vs_htrans.cpp -o vs_htrans.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o immunoClust.so 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 -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-immunoClust/00new/immunoClust/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (immunoClust)
INSTALL report for immunoClust on malbec2

Summary

Command output
