############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/immunoClust_1.24.0.tar.gz && rm -rf immunoClust.buildbin-libdir && mkdir immunoClust.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunoClust.buildbin-libdir immunoClust_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL immunoClust_1.24.0.zip && rm immunoClust_1.24.0.tar.gz immunoClust_1.24.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 449k 100 449k 0 0 1496k 0 --:--:-- --:--:-- --:--:-- 1501k 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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/immunoClust.buildbin-libdir/00LOCK-immunoClust/00new/immunoClust/libs/i386 ** R ** data ** 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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/immunoClust.buildbin-libdir/immunoClust/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'immunoClust' as immunoClust_1.24.0.zip * DONE (immunoClust) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'immunoClust' successfully unpacked and MD5 sums checked