############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL immunoClust ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-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++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_meta.cpp -o R_meta.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_model.cpp -o R_model.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c dist_mvn.cpp -o dist_mvn.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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::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++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_meta_kl.cpp -o em_meta_kl.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvn.cpp -o em_mvn.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvt.cpp -o em_mvt.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c em_mvt2.cpp -o em_mvt2.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hc_meta.cpp -o hc_meta.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c immunoClust.c -o immunoClust.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c meta_norm.cpp -o meta_norm.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c meta_scale.cpp -o meta_scale.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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::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++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c sub_mvn.cpp -o sub_mvn.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c vs_htrans.cpp -o vs_htrans.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o immunoClust.so 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 -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-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)