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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL FindMyFriends
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* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘FindMyFriends’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(std::size_t, std::size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:156:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
cdhit-common.cpp:170:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
cdhit-common.cpp:2407:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
^
cdhit-common.cpp:2424:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
^
cdhit-common.cpp:2426:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
^
cdhit-common.cpp:2447:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
cdhit-common.cpp:2456:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
^
cdhit-common.cpp:2481:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
^
cdhit-common.cpp:3140:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
^
In file included from cdhit-common.cpp:37:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-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<int>&, Vector<unsigned int>&, NVector<IndexCount>&, NVector<unsigned int>&, 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 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 between signed and unsigned integer expressions [-Wsign-compare]
if (len > max_len) max_len = len;
^
cdhit-common.cpp:1766:11: warning: comparison between signed and unsigned integer expressions [-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<int, std::allocator<int> > 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<INTs> & aap_list = buf.aap_list;
^
cdhit-common.cpp:2537:17: warning: unused variable ‘aap_begin’ [-Wunused-variable]
Vector<INTs> & aap_begin = buf.aap_begin;
^
cdhit-common.cpp:2539:17: warning: unused variable ‘taap’ [-Wunused-variable]
Vector<int> & 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<INTs> & aap_list = buf.aap_list;
^
cdhit-common.cpp:2700:17: warning: unused variable ‘aap_begin’ [-Wunused-variable]
Vector<INTs> & aap_begin = buf.aap_begin;
^
cdhit-common.cpp:2702:17: warning: unused variable ‘taap’ [-Wunused-variable]
Vector<int> & 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 );
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c fastaFunctions.cpp -o fastaFunctions.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < geneRelation.size(); ++i) {
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c linearKernel.cpp -o linearKernel.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c neighborhoodSim.cpp -o neighborhoodSim.o
neighborhoodSim.cpp: In function ‘void filterNeighborhood(std::vector<int>, std::vector<int>, std::vector<int>&)’:
neighborhoodSim.cpp:36:23: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
for (l = 0; l < lookupMap[group[k]].size(); ++l) {
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -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;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c progress.cpp -o progress.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c smallgraph.cpp -o smallgraph.o
smallgraph.cpp: In member function ‘void Graph::deleteNodes(std::vector<int>)’:
smallgraph.cpp:34:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < ids.size(); ++i) {
^
smallgraph.cpp:41:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < ids.size(); ++i) {
^
smallgraph.cpp:53:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = next_possible_edge; i < valid_edge.size(); ++i) {
^
smallgraph.cpp: In member function ‘void Graph::deleteEdges(std::vector<int>)’:
smallgraph.cpp:66:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < ids.size(); ++i) {
^
smallgraph.cpp: In member function ‘std::pair<int, int> Graph::firstEdge()’:
smallgraph.cpp:100:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = next_possible_edge; i < valid_edge.size(); ++i) {
^
smallgraph.cpp: In member function ‘std::vector<std::pair<int, int> > Graph::completeTriangle(std::pair<int, int>)’:
smallgraph.cpp:129:36: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
if (itmap->second.size() != maxNeighbors) {
^
smallgraph.cpp: In member function ‘std::vector<int> Graph::incidentEdges(int)’:
smallgraph.cpp:166:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = next_possible_edge; i < valid_edge.size(); ++i) {
^
smallgraph.cpp: In member function ‘std::vector<int> Graph::edgeIds()’:
smallgraph.cpp:184:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = next_possible_edge; i < valid_edge.size(); ++i) {
^
smallgraph.cpp: In member function ‘std::pair<int, int> Graph::getEdge(int)’:
smallgraph.cpp:191:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (id >= valid_edge.size() || !valid_edge[id]) {
^
smallgraph.cpp: In member function ‘void Graph::show()’:
smallgraph.cpp:199:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < valid_edge.size(); ++i) {
^
smallgraph.cpp:208:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int k = 0; k < itmap->second.size(); ++k) {
^
smallgraph.cpp:210:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k != itmap->second.size()-1) Rcout << ", ";
^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o FindMyFriends.so 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 -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/FindMyFriends/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FindMyFriends)
