############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CellaRepertorium_1.2.0.tar.gz && rm -rf CellaRepertorium.buildbin-libdir && mkdir CellaRepertorium.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellaRepertorium.buildbin-libdir CellaRepertorium_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CellaRepertorium_1.2.0.zip && rm CellaRepertorium_1.2.0.tar.gz CellaRepertorium_1.2.0.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 72 1430k 72 1036k 0 0 2024k 0 --:--:-- --:--:-- --:--:-- 2023k 100 1430k 100 1430k 0 0 2422k 0 --:--:-- --:--:-- --:--:-- 2423k install for i386 * installing *source* package 'CellaRepertorium' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-bombs.cpp -o cdhit-bombs.o In file included from cdhit-bombs.cpp:2: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-common.cpp -o cdhit-common.o cdhit-common.cpp:160: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:174: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:2418: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:2435: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:2437: warning: ignoring #pragma omp flush [-Wunknown-pragmas] #pragma omp flush (stop) cdhit-common.cpp:2458: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:2467: warning: ignoring #pragma omp flush [-Wunknown-pragmas] #pragma omp flush (stop) cdhit-common.cpp:2492: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:3151: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) In file included from cdhit-common.cpp:37: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)': cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable] int max_diag = 0; ^~~~~~~~ cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)': cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable] int max_diag = 0; ^~~~~~~~ cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)': cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] if (len > max_len) max_len = len; ~~~~^~~~~~~~~ cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] if (len < min_len) min_len = len; ~~~~^~~~~~~~~ cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)': cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable] size_t mem, mega = 1000000; ^~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-est.cpp -o cdhit-est.o In file included from cdhit-est.cpp:32: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit.cpp -o cdhit.o In file included from cdhit.cpp:31: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progress.cpp -o progress.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -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/CellaRepertorium.buildbin-libdir/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CellaRepertorium' finding HTML links ... done ContigCellDB-fun html canonicalize_cell html canonicalize_cluster html cash-ContigCellDB-method html ccdb_ex html ccdb_join html cdhit html cdhit_ccdb html cluster_filterset html cluster_germline html cluster_logistic_test html cluster_permute_test html cluster_plot html contigs_qc html crosstab_by_celltype html dot-cluster_permute_test html entropy html enumerate_pairing html equalize_ccdb html fancy_name_contigs html fine_cluster_seqs html fine_clustering html generate_pseudobulk html guess_celltype html hushWarning html left_join_warn html map_axis_labels html mutate_cdb html pairing_tables html purity html rank_prevalence_ccdb html rbind-ContigCellDB-method html split_cdb html sub-sub-ContigCellDB-character-missing-method html *** copying figures ** 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 'CellaRepertorium' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-bombs.cpp -o cdhit-bombs.o In file included from cdhit-bombs.cpp:2: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-common.cpp -o cdhit-common.o cdhit-common.cpp:160: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:174: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:2418: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:2435: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:2437: warning: ignoring #pragma omp flush [-Wunknown-pragmas] #pragma omp flush (stop) cdhit-common.cpp:2458: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:2467: warning: ignoring #pragma omp flush [-Wunknown-pragmas] #pragma omp flush (stop) cdhit-common.cpp:2492: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:3151: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) In file included from cdhit-common.cpp:37: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)': cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable] int max_diag = 0; ^~~~~~~~ cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)': cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable] int max_diag = 0; ^~~~~~~~ cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)': cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if (len > max_len) max_len = len; ~~~~^~~~~~~~~ cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare] if (len < min_len) min_len = len; ~~~~^~~~~~~~~ cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)': cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable] size_t mem, mega = 1000000; ^~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit-est.cpp -o cdhit-est.o In file included from cdhit-est.cpp:32: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cdhit.cpp -o cdhit.o In file included from cdhit.cpp:31: cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)': cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare] if( band > options.band_width ) band = options.band_width; ~~~~~^~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progress.cpp -o progress.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -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/CellaRepertorium.buildbin-libdir/CellaRepertorium/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CellaRepertorium' as CellaRepertorium_1.2.0.zip * DONE (CellaRepertorium) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'CellaRepertorium' successfully unpacked and MD5 sums checked