############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CellaRepertorium ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘CellaRepertorium’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit-common.cpp -o cdhit-common.o cdhit-common.cpp:160: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 160 | #pragma omp critical | cdhit-common.cpp:174: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 174 | #pragma omp critical | cdhit-common.cpp:2418: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2418 | #pragma omp parallel for schedule( dynamic, 1 ) | cdhit-common.cpp:2435: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2435 | #pragma omp parallel for schedule( dynamic, 1 ) | cdhit-common.cpp:2437: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 2437 | #pragma omp flush (stop) | cdhit-common.cpp:2458: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 2458 | #pragma omp critical | cdhit-common.cpp:2467: warning: ignoring ‘#pragma omp flush’ [-Wunknown-pragmas] 2467 | #pragma omp flush (stop) | cdhit-common.cpp:2492: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2492 | #pragma omp parallel for schedule( dynamic, 1 ) | cdhit-common.cpp:3151: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3151 | #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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | 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:545:13: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable] 545 | 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:669:13: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable] 669 | int max_diag = 0; | ^~~~~~~~ cdhit-common.cpp: In member function ‘void SequenceDB::SortDivide(Options&, bool)’: cdhit-common.cpp:1774:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1774 | if (len > max_len) max_len = len; | ~~~~^~~~~~~~~ cdhit-common.cpp:1775:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1775 | if (len < min_len) min_len = len; | ~~~~^~~~~~~~~ cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(int, const Options&)’: cdhit-common.cpp:2379:16: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable] 2379 | size_t mem, mega = 1000000; | ^~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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:494:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c progress.cpp -o progress.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o CellaRepertorium.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'CellaRepertorium' is deprecated and will be removed from Bioconductor version 3.21 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'CellaRepertorium' is deprecated and will be removed from Bioconductor version 3.21 ** testing if installed package keeps a record of temporary installation path * DONE (CellaRepertorium)