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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).

INSTALL results for FindMyFriends on tokay2

To the developers/maintainers of the FindMyFriends package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindMyFriends.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 634/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindMyFriends 1.22.0  (landing page)
Thomas Lin Pedersen
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/FindMyFriends
git_branch: RELEASE_3_13
git_last_commit: 526b1e4
git_last_commit_date: 2021-05-19 12:15:44 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: FindMyFriends
Version: 1.22.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/FindMyFriends_1.22.0.tar.gz && rm -rf FindMyFriends.buildbin-libdir && mkdir FindMyFriends.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FindMyFriends.buildbin-libdir FindMyFriends_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FindMyFriends_1.22.0.zip && rm FindMyFriends_1.22.0.tar.gz FindMyFriends_1.22.0.zip
StartedAt: 2021-10-14 11:17:40 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:20:53 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 193.1 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/FindMyFriends_1.22.0.tar.gz && rm -rf FindMyFriends.buildbin-libdir && mkdir FindMyFriends.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FindMyFriends.buildbin-libdir FindMyFriends_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FindMyFriends_1.22.0.zip && rm FindMyFriends_1.22.0.tar.gz FindMyFriends_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 64 1715k   64 1110k    0     0  1565k      0  0:00:01 --:--:--  0:00:01 1565k
100 1715k  100 1715k    0     0  1768k      0 --:--:-- --:--:-- --:--:-- 1768k

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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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  
    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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/FindMyFriends.buildbin-libdir/FindMyFriends/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FindMyFriends' as FindMyFriends_1.22.0.zip
* DONE (FindMyFriends)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'FindMyFriends' successfully unpacked and MD5 sums checked