############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r FindMyFriends -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data FindMyFriends ### ############################################################################## ############################################################################## * checking for file 'FindMyFriends/DESCRIPTION' ... OK * preparing 'FindMyFriends': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package 'FindMyFriends' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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:488:12: 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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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:156: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:170: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:2407: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:2424: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:2426: warning: ignoring #pragma omp flush [-Wunknown-pragmas] #pragma omp flush (stop) cdhit-common.cpp:2447: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical cdhit-common.cpp:2456: warning: ignoring #pragma omp flush [-Wunknown-pragmas] #pragma omp flush (stop) cdhit-common.cpp:2481: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for schedule( dynamic, 1 ) cdhit-common.cpp:3140: 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:488:12: 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 member function 'bool Options::SetOptions(int, char**, bool, bool)': cdhit-common.cpp:341:9: warning: unused variable 'tm' [-Wunused-variable] time_t tm = time(NULL); ^~ cdhit-common.cpp: In member function 'void Options::Validate()': cdhit-common.cpp:394:14: warning: unused variable 'message' [-Wunused-variable] const char *message = "Your word length is %i, using %i may be faster!\n"; ^~~~~~~ cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)': cdhit-common.cpp:517:8: warning: unused variable 'bip' [-Wunused-variable] INTs *bip; ^~~ cdhit-common.cpp:540:6: 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:664:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable] int max_diag = 0; ^~~~~~~~ cdhit-common.cpp: In function 'int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)': cdhit-common.cpp:866:8: warning: unused variable 's1' [-Wunused-variable] int s1, k0, back; ^~ cdhit-common.cpp:866:12: warning: unused variable 'k0' [-Wunused-variable] int s1, k0, back; ^~ cdhit-common.cpp:777:6: warning: unused variable 'jj' [-Wunused-variable] int jj, kk; ^~ cdhit-common.cpp:777:10: warning: unused variable 'kk' [-Wunused-variable] int jj, kk; ^~ cdhit-common.cpp:778:6: warning: unused variable 'iden_no1' [-Wunused-variable] int iden_no1; ^~~~~~~~ cdhit-common.cpp:917:14: warning: unused variable 'letters' [-Wunused-variable] const char *letters = "acgtnx"; ^~~~~~~ cdhit-common.cpp:918:14: warning: unused variable 'letters2' [-Wunused-variable] const char *letters2 = "ACGTNX"; ^~~~~~~~ cdhit-common.cpp: In member function 'void ScoreMatrix::set_gap(int, int)': cdhit-common.cpp:1200:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ cdhit-common.cpp: In member function 'int WordTable::CountWords(int, Vector&, Vector&, NVector&, NVector&, bool, int)': cdhit-common.cpp:1417:6: warning: unused variable 'S' [-Wunused-variable] int S = frag_count ? frag_count : sequences.size(); ^ cdhit-common.cpp:1418:25: warning: unused variable 'm' [-Wunused-variable] int j, k, j0, j1, k1, m; ^ cdhit-common.cpp:1419:6: warning: unused variable 'ix1' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^~~ cdhit-common.cpp:1419:11: warning: unused variable 'ix2' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^~~ cdhit-common.cpp:1419:16: warning: unused variable 'ix3' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^~~ cdhit-common.cpp:1419:21: warning: unused variable 'ix4' [-Wunused-variable] int ix1, ix2, ix3, ix4; ^~~ cdhit-common.cpp: In copy constructor 'Sequence::Sequence(const Sequence&)': cdhit-common.cpp:1469:6: warning: unused variable 'i' [-Wunused-variable] int i; ^ cdhit-common.cpp: In member function 'void Sequence::operator+=(const char*)': cdhit-common.cpp:1511:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size, n = strlen( s ); ^ cdhit-common.cpp: In member function 'void Sequence::Resize(int)': cdhit-common.cpp:1517:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size < n ? size : n; ^ cdhit-common.cpp: In member function 'void Sequence::Reserve(int)': cdhit-common.cpp:1533:6: warning: unused variable 'i' [-Wunused-variable] int i, m = size < n ? size : n; ^ cdhit-common.cpp: In member function 'void Sequence::Swap(Sequence&)': cdhit-common.cpp:1556:42: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Sequence'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy( & tmp, this, sizeof( Sequence ) ); ^ In file included from cdhit-common.cpp:37: cdhit-common.h:364:8: note: 'struct Sequence' declared here struct Sequence ^~~~~~~~ cdhit-common.cpp:1558:45: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of non-trivially copyable type 'struct Sequence'; use copy-assignment or copy-initialization instead [-Wclass-memaccess] memcpy( & other, & tmp, sizeof( Sequence ) ); ^ In file included from cdhit-common.cpp:37: cdhit-common.h:364:8: note: 'struct Sequence' declared here struct Sequence ^~~~~~~~ cdhit-common.cpp:1559:39: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct Sequence'; use assignment or value-initialization instead [-Wclass-memaccess] memset( & tmp, 0, sizeof( Sequence ) ); ^ In file included from cdhit-common.cpp:37: cdhit-common.h:364:8: note: 'struct Sequence' declared here struct Sequence ^~~~~~~~ cdhit-common.cpp: In member function 'void SequenceDB::Read(const char*, const Options&)': cdhit-common.cpp:1622:12: warning: unused variable 'last' [-Wunused-variable] Sequence *last = NULL; ^~~~ cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)': cdhit-common.cpp:1765:11: 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:1766:11: 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:1755:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k, len; ^ cdhit-common.cpp:1755:12: warning: unused variable 'k' [-Wunused-variable] int i, j, k, len; ^ cdhit-common.cpp: In member function 'std::vector > SequenceDB::GetClusters(const Options&)': cdhit-common.cpp:1944:12: warning: unused variable 'k' [-Wunused-variable] int i, k, N = sequences.size(); ^ cdhit-common.cpp: In member function 'void WorkingParam::ComputeRequiredBases(int, int, const Options&)': cdhit-common.cpp:2098:7: warning: unused variable 'k' [-Wunused-variable] int k = len_eff < invd ? len_eff : invd; ^ cdhit-common.cpp:2103:7: warning: unused variable 'ks3' [-Wunused-variable] int ks3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * ss)); ^~~ cdhit-common.cpp:2104:7: warning: unused variable 'kn3' [-Wunused-variable] int kn3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * NAA)); ^~~ cdhit-common.cpp: In member function 'void SequenceDB::ClusterOne(Sequence*, int, WordTable&, WorkingParam&, WorkingBuffer&, const Options&)': cdhit-common.cpp:2255:7: warning: unused variable 'size' [-Wunused-variable] int size = rep_seqs.size(); ^~~~ cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)': cdhit-common.cpp:2329:9: warning: unused variable 'j' [-Wunused-variable] int i, j, k; ^ cdhit-common.cpp:2337:6: warning: unused variable 'len' [-Wunused-variable] int len, len_bound; ^~~ cdhit-common.cpp:2337:11: warning: unused variable 'len_bound' [-Wunused-variable] int len, len_bound; ^~~~~~~~~ cdhit-common.cpp:2338:6: warning: unused variable 'flag' [-Wunused-variable] int flag; ^~~~ cdhit-common.cpp:2365:6: warning: unused variable 'K' [-Wunused-variable] int K = N - 100 * T; ^ cdhit-common.cpp:2367:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^~~~~~~~~ cdhit-common.cpp:2368:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable] size_t mem, mega = 1000000; ^~~ cdhit-common.cpp: In member function 'int SequenceDB::CheckOneAA(Sequence*, WordTable&, WorkingParam&, WorkingBuffer&, const Options&)': cdhit-common.cpp:2536:17: warning: unused variable 'aap_list' [-Wunused-variable] Vector & aap_list = buf.aap_list; ^~~~~~~~ cdhit-common.cpp:2537:17: warning: unused variable 'aap_begin' [-Wunused-variable] Vector & aap_begin = buf.aap_begin; ^~~~~~~~~ cdhit-common.cpp:2539:17: warning: unused variable 'taap' [-Wunused-variable] Vector & taap = buf.taap; ^~~~ cdhit-common.cpp:2545:6: warning: unused variable 'j' [-Wunused-variable] int j, k, j1, len = seq->size; ^ cdhit-common.cpp:2579:6: warning: unused variable 'M' [-Wunused-variable] int M = frag_size ? table.frag_count : S; ^ cdhit-common.cpp:2589:6: warning: unused variable 'best1' [-Wunused-variable] int best1, sum; ^~~~~ cdhit-common.cpp:2590:8: warning: unused variable 'lookptr' [-Wunused-variable] INTs *lookptr; ^~~~~~~ cdhit-common.cpp: In member function 'int SequenceDB::CheckOneEST(Sequence*, WordTable&, WorkingParam&, WorkingBuffer&, const Options&)': cdhit-common.cpp:2699:17: warning: unused variable 'aap_list' [-Wunused-variable] Vector & aap_list = buf.aap_list; ^~~~~~~~ cdhit-common.cpp:2700:17: warning: unused variable 'aap_begin' [-Wunused-variable] Vector & aap_begin = buf.aap_begin; ^~~~~~~~~ cdhit-common.cpp:2702:17: warning: unused variable 'taap' [-Wunused-variable] Vector & taap = buf.taap; ^~~~ cdhit-common.cpp: In member function 'void SequenceDB::ComputeDistance(const Options&)': cdhit-common.cpp:2876:55: warning: unused variable 'required_aa1' [-Wunused-variable] int band_width1, band_left, band_center, band_right, required_aa1; ^~~~~~~~~~~~ cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(const Options&, std::__cxx11::string, bool)': cdhit-common.cpp:3024:9: warning: unused variable 'p0' [-Wunused-variable] float p0 = 0; ^~ cdhit-common.cpp:2949:6: warning: unused variable 'len' [-Wunused-variable] int len, len_bound; ^~~ cdhit-common.cpp:2949:11: warning: unused variable 'len_bound' [-Wunused-variable] int len, len_bound; ^~~~~~~~~ cdhit-common.cpp:2950:6: warning: unused variable 'flag' [-Wunused-variable] int flag; ^~~~ cdhit-common.cpp:2978:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^~~~~~~~~ cdhit-common.cpp:2979:9: warning: unused variable 'mem' [-Wunused-variable] size_t mem, mega = 1000000; ^~~ cdhit-common.cpp:2979:14: warning: unused variable 'mega' [-Wunused-variable] size_t mem, mega = 1000000; ^~~~ cdhit-common.cpp: In member function 'void SequenceDB::ClusterTo(SequenceDB&, const Options&)': cdhit-common.cpp:3145:11: warning: unused variable 'seqi' [-Wunused-variable] char *seqi = seq->data; ^~~~ cdhit-common.cpp:3063:9: warning: unused variable 'is' [-Wunused-variable] int i, is, js, flag; ^~ cdhit-common.cpp:3063:13: warning: unused variable 'js' [-Wunused-variable] int i, is, js, flag; ^~ cdhit-common.cpp:3097:9: warning: unused variable 'mem_limit' [-Wunused-variable] size_t mem_limit = MemoryLimit( mem_need, options ); ^~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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:488:12: 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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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:488:12: 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-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastaFunctions.cpp -o fastaFunctions.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fmf-common.cpp -o fmf-common.o fmf-common.cpp: In function 'Rcpp::List createPanMatrix(Rcpp::IntegerVector, Rcpp::IntegerVector)': fmf-common.cpp:24:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::deque >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i = 0; i < geneRelation.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linearKernel.cpp -o linearKernel.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c neighborhoodSim.cpp -o neighborhoodSim.o neighborhoodSim.cpp: In function 'void filterNeighborhood(std::vector, std::vector, std::vector&)': neighborhoodSim.cpp:36:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < neighborhood.size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~ neighborhoodSim.cpp: In function 'Rcpp::List neighborhoodSim(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::LogicalVector, Rcpp::IntegerVector, double, bool)': neighborhoodSim.cpp:113:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (k = 0; k < neighborhoodI.size(); k++) { ~~^~~~~~~~~~~~~~~~~~~~~~ neighborhoodSim.cpp: In function 'Rcpp::LogicalVector groupHasParalogues(Rcpp::List, Rcpp::IntegerVector)': neighborhoodSim.cpp:443:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (currentOrg < visited.size() && visited[currentOrg]) { ~~~~~~~~~~~^~~~~~~~~~~~~~~~ neighborhoodSim.cpp:432:9: warning: unused variable 'maxO' [-Wunused-variable] int maxO = 0; ^~~~ neighborhoodSim.cpp: In function 'Rcpp::DataFrame mergeGroupsByNeighbors(Rcpp::List, Rcpp::DataFrame)': neighborhoodSim.cpp:519:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (l = 0; l < lookupMap[group[k]].size(); ++l) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c panSim.cpp -o panSim.o panSim.cpp: In function 'Rcpp::NumericMatrix panSim(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::CharacterVector)': panSim.cpp:16:9: warning: unused variable 'k' [-Wunused-variable] int k; ^ panSim.cpp:19:9: warning: unused variable 'iVal' [-Wunused-variable] int iVal; ^~~~ panSim.cpp:20:9: warning: unused variable 'jVal' [-Wunused-variable] int jVal; ^~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-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 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c smallgraph.cpp -o smallgraph.o smallgraph.cpp: In member function 'void Graph::deleteNodes(std::vector)': smallgraph.cpp:34:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i = 0; i < ids.size(); ++i) { ~~^~~~~~~~~~~~ smallgraph.cpp:41:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i = 0; i < ids.size(); ++i) { ~~^~~~~~~~~~~~ smallgraph.cpp:53:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i = next_possible_edge; i < valid_edge.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'void Graph::deleteEdges(std::vector)': smallgraph.cpp:66:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < ids.size(); ++i) { ~~^~~~~~~~~~~~ smallgraph.cpp: In member function 'std::pair Graph::firstEdge()': smallgraph.cpp:100:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i = next_possible_edge; i < valid_edge.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'std::vector > Graph::completeTriangle(std::pair)': smallgraph.cpp:129:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i = next_possible_edge; i < valid_edge.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'bool Graph::isComplete()': smallgraph.cpp:145:34: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if (itmap->second.size() != maxNeighbors) { ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'std::vector Graph::incidentEdges(int)': smallgraph.cpp:166:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = next_possible_edge; i < valid_edge.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'std::vector Graph::edgeIds()': smallgraph.cpp:184:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = next_possible_edge; i < valid_edge.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'std::pair Graph::getEdge(int)': smallgraph.cpp:191:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (id >= valid_edge.size() || !valid_edge[id]) { ~~~^~~~~~~~~~~~~~~~~~~~ smallgraph.cpp: In member function 'void Graph::show()': smallgraph.cpp:199:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int i = 0; i < valid_edge.size(); ++i) { ~~^~~~~~~~~~~~~~~~~~~ smallgraph.cpp:208:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (int k = 0; k < itmap->second.size(); ++k) { ~~^~~~~~~~~~~~~~~~~~~~~~ smallgraph.cpp:210:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if (k != itmap->second.size()-1) Rcout << ", "; ~~^~~~~~~~~~~~~~~~~~~~~~~~~ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o FindMyFriends.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o fastaFunctions.o fmf-common.o linearKernel.o neighborhoodSim.o panSim.o progress.o smallgraph.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpS6rtQK/Rinst214434bd1176/00LOCK-FindMyFriends/00new/FindMyFriends/libs/x64 ** R Error in .install_package_code_files(".", instdir) : files in 'Collate' field missing from 'C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpS6rtQK/Rbuild2144209707f/FindMyFriends/R': zzz.R ERROR: unable to collate and parse R files for package 'FindMyFriends' * removing 'C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpS6rtQK/Rinst214434bd1176/FindMyFriends' ----------------------------------- ERROR: package installation failed