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###
### Running command:
###
### rm -rf FindMyFriends.buildbin-libdir && mkdir FindMyFriends.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/FindMyFriends_1.3.2.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=FindMyFriends.buildbin-libdir --merge-multiarch FindMyFriends_1.3.2.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL FindMyFriends_1.3.2.zip && rm FindMyFriends_1.3.2.tar.gz FindMyFriends_1.3.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 1716k 0 15815 0 0 4875 0 0:06:00 0:00:03 0:05:57 4882
26 1716k 26 451k 0 0 104k 0 0:00:16 0:00:04 0:00:12 104k
26 1716k 26 451k 0 0 86701 0 0:00:20 0:00:05 0:00:15 86770
27 1716k 27 477k 0 0 79684 0 0:00:22 0:00:06 0:00:16 79747
64 1716k 64 1110k 0 0 152k 0 0:00:11 0:00:07 0:00:04 183k
100 1716k 100 1716k 0 0 234k 0 0:00:07 0:00:07 --:--:-- 416k
install for i386
* installing *source* package 'FindMyFriends' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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::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:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c fastaFunctions.cpp -o fastaFunctions.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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) {
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c linearKernel.cpp -o linearKernel.o
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c neighborhoodSim.cpp -o neighborhoodSim.o
neighborhoodSim.cpp: In function 'void filterNeighborhood(std::vector<int>, std::vector<int>, std::vector<int>&)':
neighborhoodSim.cpp:35:23: 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:112:27: 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:448:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (currentOrg < visited.size() && visited[currentOrg]) {
^
neighborhoodSim.cpp:437:9: warning: unused variable 'maxO' [-Wunused-variable]
int maxO = 0;
^
neighborhoodSim.cpp: In function 'Rcpp::DataFrame mergeGroupsByNeighbors(Rcpp::List, Rcpp::DataFrame)':
neighborhoodSim.cpp:524:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (l = 0; l < lookupMap[group[k]].size(); ++l) {
^
C:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:/Rtools/mingw_32/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c progress.cpp -o progress.o
C:/Rtools/mingw_32/bin/g++ -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 -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/FindMyFriends.buildbin-libdir/FindMyFriends/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'IRanges::which' by 'Matrix::which' when loading 'FindMyFriends'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::which' by 'Matrix::which' when loading 'FindMyFriends'
install for x64
* installing *source* package 'FindMyFriends' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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::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:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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;
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c fastaFunctions.cpp -o fastaFunctions.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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) {
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c linearKernel.cpp -o linearKernel.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c neighborhoodSim.cpp -o neighborhoodSim.o
neighborhoodSim.cpp: In function 'void filterNeighborhood(std::vector<int>, std::vector<int>, std::vector<int>&)':
neighborhoodSim.cpp:35:23: 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:112:27: 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:448:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (currentOrg < visited.size() && visited[currentOrg]) {
^
neighborhoodSim.cpp:437:9: warning: unused variable 'maxO' [-Wunused-variable]
int maxO = 0;
^
neighborhoodSim.cpp: In function 'Rcpp::DataFrame mergeGroupsByNeighbors(Rcpp::List, Rcpp::DataFrame)':
neighborhoodSim.cpp:524:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (l = 0; l < lookupMap[group[k]].size(); ++l) {
^
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -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:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c progress.cpp -o progress.o
C:/Rtools/mingw_64/bin/g++ -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 -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/FindMyFriends.buildbin-libdir/FindMyFriends/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::which' by 'Matrix::which' when loading 'FindMyFriends'
* MD5 sums
packaged installation of 'FindMyFriends' as FindMyFriends_1.3.2.zip
* DONE (FindMyFriends)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'FindMyFriends' successfully unpacked and MD5 sums checked
