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This page was generated on 2022-01-14 13:06:22 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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BUILD 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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 643/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindMyFriends 1.24.0  (landing page)
Thomas Lin Pedersen
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/FindMyFriends
git_branch: RELEASE_3_14
git_last_commit: 5660a60
git_last_commit_date: 2021-10-26 12:22:45 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  ERROR    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  ERROR    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: FindMyFriends
Version: 1.24.0
Command: chmod a+r FindMyFriends -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data FindMyFriends
StartedAt: 2022-01-13 10:47:21 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 10:48:30 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 68.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: FindMyFriends_1.24.0.tar.gz
PackageFileSize: 1.677 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r FindMyFriends -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data FindMyFriends
###
##############################################################################
##############################################################################


* checking for file 'FindMyFriends/DESCRIPTION' ... OK
* preparing 'FindMyFriends':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'FindMyFriends' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:488:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:156: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
   #pragma omp critical
 
cdhit-common.cpp:170: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  #pragma omp critical
 
cdhit-common.cpp:2407: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:2424: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:2426: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
     #pragma omp flush (stop)
 
cdhit-common.cpp:2447: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
        #pragma omp critical
 
cdhit-common.cpp:2456: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
        #pragma omp flush (stop)
 
cdhit-common.cpp:2481: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:3140: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:488:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In member function 'bool Options::SetOptions(int, char**, bool, bool)':
cdhit-common.cpp:341:9: warning: unused variable 'tm' [-Wunused-variable]
  time_t tm = time(NULL);
         ^~
cdhit-common.cpp: In member function 'void Options::Validate()':
cdhit-common.cpp:394:14: warning: unused variable 'message' [-Wunused-variable]
  const char *message = "Your word length is %i, using %i may be faster!\n";
              ^~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:517:8: warning: unused variable 'bip' [-Wunused-variable]
  INTs *bip;
        ^~~
cdhit-common.cpp:540:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
  int max_diag = 0;
      ^~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:664:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
  int max_diag = 0;
      ^~~~~~~~
cdhit-common.cpp: In function 'int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)':
cdhit-common.cpp:866:8: warning: unused variable 's1' [-Wunused-variable]
    int s1, k0, back;
        ^~
cdhit-common.cpp:866:12: warning: unused variable 'k0' [-Wunused-variable]
    int s1, k0, back;
            ^~
cdhit-common.cpp:777:6: warning: unused variable 'jj' [-Wunused-variable]
  int jj, kk;
      ^~
cdhit-common.cpp:777:10: warning: unused variable 'kk' [-Wunused-variable]
  int jj, kk;
          ^~
cdhit-common.cpp:778:6: warning: unused variable 'iden_no1' [-Wunused-variable]
  int iden_no1;
      ^~~~~~~~
cdhit-common.cpp:917:14: warning: unused variable 'letters' [-Wunused-variable]
  const char *letters = "acgtnx";
              ^~~~~~~
cdhit-common.cpp:918:14: warning: unused variable 'letters2' [-Wunused-variable]
  const char *letters2 = "ACGTNX";
              ^~~~~~~~
cdhit-common.cpp: In member function 'void ScoreMatrix::set_gap(int, int)':
cdhit-common.cpp:1200:6: warning: unused variable 'i' [-Wunused-variable]
  int i;
      ^
cdhit-common.cpp: In member function 'int WordTable::CountWords(int, Vector<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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:488:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:488:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastaFunctions.cpp -o fastaFunctions.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fmf-common.cpp -o fmf-common.o
fmf-common.cpp: In function 'Rcpp::List createPanMatrix(Rcpp::IntegerVector, Rcpp::IntegerVector)':
fmf-common.cpp:24:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::deque<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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c linearKernel.cpp -o linearKernel.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c neighborhoodSim.cpp -o neighborhoodSim.o
neighborhoodSim.cpp: In function 'void filterNeighborhood(std::vector<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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c panSim.cpp -o panSim.o
panSim.cpp: In function 'Rcpp::NumericMatrix panSim(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::CharacterVector)':
panSim.cpp:16:9: warning: unused variable 'k' [-Wunused-variable]
     int k;
         ^
panSim.cpp:19:9: warning: unused variable 'iVal' [-Wunused-variable]
     int iVal;
         ^~~~
panSim.cpp:20:9: warning: unused variable 'jVal' [-Wunused-variable]
     int jVal;
         ^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progress.cpp -o progress.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c smallgraph.cpp -o smallgraph.o
smallgraph.cpp: In member function 'void Graph::deleteNodes(std::vector<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-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpkFAYBU/Rinst28542a767146/00LOCK-FindMyFriends/00new/FindMyFriends/libs/x64
** R
Error in .install_package_code_files(".", instdir) : 
files in 'Collate' field missing from 'C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpkFAYBU/Rbuild285468de54c7/FindMyFriends/R':
  zzz.R
ERROR: unable to collate and parse R files for package 'FindMyFriends'
* removing 'C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpkFAYBU/Rinst28542a767146/FindMyFriends'
      -----------------------------------
ERROR: package installation failed