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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/FindMyFriends_1.20.0.tar.gz && rm -rf FindMyFriends.buildbin-libdir && mkdir FindMyFriends.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FindMyFriends.buildbin-libdir FindMyFriends_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL FindMyFriends_1.20.0.zip && rm FindMyFriends_1.20.0.tar.gz FindMyFriends_1.20.0.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
100 1718k 100 1718k 0 0 43.4M 0 --:--:-- --:--:-- --:--:-- 45.3M
install for i386
* installing *source* package 'FindMyFriends' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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 '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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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 '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<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 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 '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 '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<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 );
^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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 '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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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 '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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fastaFunctions.cpp -o fastaFunctions.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<std::pair<int, int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (i = 0; i < geneRelation.size(); ++i) {
~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linearKernel.cpp -o linearKernel.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<int>, std::vector<int>, std::vector<int>&)':
neighborhoodSim.cpp:36:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka '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<int>::size_type' {aka '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<bool>::size_type' {aka '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<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (l = 0; l < lookupMap[group[k]].size(); ++l) {
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<int>)':
smallgraph.cpp:34:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka '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<int>::size_type' {aka '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<bool>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka '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<int>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (itmap->second.size() != maxNeighbors) {
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
smallgraph.cpp: In member function 'std::vector<int> Graph::incidentEdges(int)':
smallgraph.cpp:166:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<bool>::size_type' {aka '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<bool>::size_type' {aka '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<int>::size_type' {aka '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<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
if (k != itmap->second.size()-1) Rcout << ", ";
~~^~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/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/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/FindMyFriends.buildbin-libdir/00LOCK-FindMyFriends/00new/FindMyFriends/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'FindMyFriends'
finding HTML links ... done
FindMyFriends-package html
addGenomes html
addGroupInfo html
addOrgInfo html
cdhitGrouping html
collapseParalogues html
defaults html
fillDefaults html
geneLocation html
geneNames html
geneWidth html
genes html
getNeighborhood html
getRep html
gpcGrouping html
finding level-2 HTML links ... done
graphGrouping html
groupInfo html
groupNames html
groupStat html
hasGeneGroups html
hasGeneInfo html
hasParalogueLinks html
internalGroupGenes html
internalMergePangenomes html
internalMetadata html
kmerLink html
kmerSimilarity html
kmerSplit html
loadPgExample html
manualGrouping html
nGeneGroups html
nGenes html
nOrganisms html
neighborhoodSplit html
orgInfo html
orgNames html
orgStat html
pangenome html
pcGraph html
pgFull-class html
pgFullLoc-class html
pgInMem-class html
pgInMemLoc-class html
pgLM-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp42Vk1P/R.INSTALL3028e583f88/FindMyFriends/man/pgLM-class.Rd:20: file link 'fasta.index' in package 'Biostrings' does not exist and so has been treated as a topic
pgLMLoc-class html
pgMatrix html
pgSlim-class html
pgSlimLoc-class html
pgVirtual-class html
pgVirtualLoc-class html
plotEvolution html
plotGroup html
plotNeighborhood html
plotSimilarity html
plotStat html
plotTree html
readAnnot html
removeGene html
reportGroupChanges html
seqToGeneGroup html
seqToOrg html
translated html
variableRegions html
** 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 'FindMyFriends' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<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 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<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 );
^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<std::pair<int, int> >::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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<int>, std::vector<int>, std::vector<int>&)':
neighborhoodSim.cpp:36:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::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<int>::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<bool>::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<int>::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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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<int>)':
smallgraph.cpp:34:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::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<int>::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<bool>::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<int>)':
smallgraph.cpp:66:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<bool>::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<std::pair<int, int> > Graph::completeTriangle(std::pair<int, int>)':
smallgraph.cpp:129:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::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<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if (itmap->second.size() != maxNeighbors) {
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
smallgraph.cpp: In member function 'std::vector<int> Graph::incidentEdges(int)':
smallgraph.cpp:166:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::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<int> Graph::edgeIds()':
smallgraph.cpp:184:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::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<int, int> Graph::getEdge(int)':
smallgraph.cpp:191:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<bool>::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<bool>::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<int>::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<int>::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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/FindMyFriends.buildbin-libdir/FindMyFriends/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FindMyFriends' as FindMyFriends_1.20.0.zip
* DONE (FindMyFriends)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'FindMyFriends' successfully unpacked and MD5 sums checked
