Package: FindMyFriends

Version: 1.13.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FindMyFriends_1.13.0.tar.gz

StartedAt: 2019-04-09 00:28:52 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:37:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 503.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: FindMyFriends.Rcheck

Warnings: NA

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FindMyFriends_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/FindMyFriends.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FindMyFriends/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FindMyFriends’ version ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FindMyFriends’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      5.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘gtable:::insert.unit’ ‘gtable:::z_arrange_gtables’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'pgVirtual-class' but not in code:
  as

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kmerLink  6.696  0.036   7.188
groupStat 5.991  0.112   6.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 2. Error: kmerSimilarity works (@test-similarities.R#9)  ────────────────────
  non-numeric argument to binary operator
  1: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam()) at testthat/test-similarities.R:9
  2: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam())
  3: .local(object, ...)
  4: lkParallel(er, pParam, bpworkers(pParam), lowerLimit = lowerLimit)
  5: getChunks(nrow(x), nSplits)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 288 SKIPPED: 1 FAILED: 2
  1. Error: kmerLink works (@test-linking.R#9) 
  2. Error: kmerSimilarity works (@test-similarities.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/FindMyFriends.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL FindMyFriends
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘FindMyFriends’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:156:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
   #pragma omp critical
 
cdhit-common.cpp:170:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  #pragma omp critical
 
cdhit-common.cpp:2407:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:2424:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:2426:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
     #pragma omp flush (stop)
 
cdhit-common.cpp:2447:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
        #pragma omp critical
 
cdhit-common.cpp:2456:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
        #pragma omp flush (stop)
 
cdhit-common.cpp:2481:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:3140:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
In file included from cdhit-common.cpp:37:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cdhit-common.cpp: In member function ‘bool Options::SetOptions(int, char**, bool, bool)’:
cdhit-common.cpp:341:9: warning: unused variable ‘tm’ [-Wunused-variable]
  time_t tm = time(NULL);
         ^˜
cdhit-common.cpp: In member function ‘void Options::Validate()’:
cdhit-common.cpp:394:14: warning: unused variable ‘message’ [-Wunused-variable]
  const char *message = "Your word length is %i, using %i may be faster!\n";
              ^˜˜˜˜˜˜
cdhit-common.cpp: In function ‘int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)’:
cdhit-common.cpp:517:8: warning: unused variable ‘bip’ [-Wunused-variable]
  INTs *bip;
        ^˜˜
cdhit-common.cpp:540:6: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
  int max_diag = 0;
      ^˜˜˜˜˜˜˜
cdhit-common.cpp: In function ‘int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)’:
cdhit-common.cpp:664:6: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
  int max_diag = 0;
      ^˜˜˜˜˜˜˜
cdhit-common.cpp: In function ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’:
cdhit-common.cpp:866:8: warning: unused variable ‘s1’ [-Wunused-variable]
    int s1, k0, back;
        ^˜
cdhit-common.cpp:866:12: warning: unused variable ‘k0’ [-Wunused-variable]
    int s1, k0, back;
            ^˜
cdhit-common.cpp:777:6: warning: unused variable ‘jj’ [-Wunused-variable]
  int jj, kk;
      ^˜
cdhit-common.cpp:777:10: warning: unused variable ‘kk’ [-Wunused-variable]
  int jj, kk;
          ^˜
cdhit-common.cpp:778:6: warning: unused variable ‘iden_no1’ [-Wunused-variable]
  int iden_no1;
      ^˜˜˜˜˜˜˜
cdhit-common.cpp:917:14: warning: unused variable ‘letters’ [-Wunused-variable]
  const char *letters = "acgtnx";
              ^˜˜˜˜˜˜
cdhit-common.cpp:918:14: warning: unused variable ‘letters2’ [-Wunused-variable]
  const char *letters2 = "ACGTNX";
              ^˜˜˜˜˜˜˜
cdhit-common.cpp: In member function ‘void ScoreMatrix::set_gap(int, int)’:
cdhit-common.cpp:1200:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i;
      ^
cdhit-common.cpp: In member function ‘int WordTable::CountWords(int, Vector<int>&, Vector<unsigned int>&, NVector<IndexCount>&, NVector<unsigned int>&, bool, int)’:
cdhit-common.cpp:1417:6: warning: unused variable ‘S’ [-Wunused-variable]
  int S = frag_count ? frag_count : sequences.size();
      ^
cdhit-common.cpp:1418:25: warning: unused variable ‘m’ [-Wunused-variable]
  int  j, k, j0, j1, k1, m;
                         ^
cdhit-common.cpp:1419:6: warning: unused variable ‘ix1’ [-Wunused-variable]
  int ix1, ix2, ix3, ix4;
      ^˜˜
cdhit-common.cpp:1419:11: warning: unused variable ‘ix2’ [-Wunused-variable]
  int ix1, ix2, ix3, ix4;
           ^˜˜
cdhit-common.cpp:1419:16: warning: unused variable ‘ix3’ [-Wunused-variable]
  int ix1, ix2, ix3, ix4;
                ^˜˜
cdhit-common.cpp:1419:21: warning: unused variable ‘ix4’ [-Wunused-variable]
  int ix1, ix2, ix3, ix4;
                     ^˜˜
cdhit-common.cpp: In copy constructor ‘Sequence::Sequence(const Sequence&)’:
cdhit-common.cpp:1469:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i;
      ^
cdhit-common.cpp: In member function ‘void Sequence::operator+=(const char*)’:
cdhit-common.cpp:1511:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i, m = size, n = strlen( s );
      ^
cdhit-common.cpp: In member function ‘void Sequence::Resize(int)’:
cdhit-common.cpp:1517:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i, m = size < n ? size : n;
      ^
cdhit-common.cpp: In member function ‘void Sequence::Reserve(int)’:
cdhit-common.cpp:1533:6: warning: unused variable ‘i’ [-Wunused-variable]
  int i, m = size < n ? size : n;
      ^
cdhit-common.cpp: In member function ‘void SequenceDB::Read(const char*, const Options&)’:
cdhit-common.cpp:1622:12: warning: unused variable ‘last’ [-Wunused-variable]
  Sequence *last = NULL;
            ^˜˜˜
cdhit-common.cpp: In member function ‘void SequenceDB::SortDivide(Options&, bool)’:
cdhit-common.cpp:1765:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (len > max_len) max_len = len;
       ˜˜˜˜^˜˜˜˜˜˜˜˜
cdhit-common.cpp:1766:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (len < min_len) min_len = len;
       ˜˜˜˜^˜˜˜˜˜˜˜˜
cdhit-common.cpp:1755:9: warning: unused variable ‘j’ [-Wunused-variable]
  int i, j, k, len;
         ^
cdhit-common.cpp:1755:12: warning: unused variable ‘k’ [-Wunused-variable]
  int i, j, k, len;
            ^
cdhit-common.cpp: In member function ‘std::vector<int, std::allocator<int> > SequenceDB::GetClusters(const Options&)’:
cdhit-common.cpp:1944:12: warning: unused variable ‘k’ [-Wunused-variable]
     int i, k, N = sequences.size();
            ^
cdhit-common.cpp: In member function ‘void WorkingParam::ComputeRequiredBases(int, int, const Options&)’:
cdhit-common.cpp:2098:7: warning: unused variable ‘k’ [-Wunused-variable]
   int k = len_eff < invd ? len_eff : invd;
       ^
cdhit-common.cpp:2103:7: warning: unused variable ‘ks3’ [-Wunused-variable]
   int ks3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * ss));
       ^˜˜
cdhit-common.cpp:2104:7: warning: unused variable ‘kn3’ [-Wunused-variable]
   int kn3 = int((len_eff - band + 1.0)*(1.0 - options.distance_thd * NAA));
       ^˜˜
cdhit-common.cpp: In member function ‘void SequenceDB::ClusterOne(Sequence*, int, WordTable&, WorkingParam&, WorkingBuffer&, const Options&)’:
cdhit-common.cpp:2255:7: warning: unused variable ‘size’ [-Wunused-variable]
   int size = rep_seqs.size();
       ^˜˜˜
cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(int, const Options&)’:
cdhit-common.cpp:2329:9: warning: unused variable ‘j’ [-Wunused-variable]
  int i, j, k;
         ^
cdhit-common.cpp:2337:6: warning: unused variable ‘len’ [-Wunused-variable]
  int len, len_bound;
      ^˜˜
cdhit-common.cpp:2337:11: warning: unused variable ‘len_bound’ [-Wunused-variable]
  int len, len_bound;
           ^˜˜˜˜˜˜˜˜
cdhit-common.cpp:2338:6: warning: unused variable ‘flag’ [-Wunused-variable]
  int flag;
      ^˜˜˜
cdhit-common.cpp:2365:6: warning: unused variable ‘K’ [-Wunused-variable]
  int K = N - 100 * T;
      ^
cdhit-common.cpp:2367:9: warning: unused variable ‘mem_limit’ [-Wunused-variable]
  size_t mem_limit = MemoryLimit( mem_need, options );
         ^˜˜˜˜˜˜˜˜
cdhit-common.cpp:2368:9: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable]
  size_t mem, mega = 1000000;
         ^˜˜
cdhit-common.cpp: In member function ‘int SequenceDB::CheckOneAA(Sequence*, WordTable&, WorkingParam&, WorkingBuffer&, const Options&)’:
cdhit-common.cpp:2536:17: warning: unused variable ‘aap_list’ [-Wunused-variable]
  Vector<INTs> & aap_list = buf.aap_list;
                 ^˜˜˜˜˜˜˜
cdhit-common.cpp:2537:17: warning: unused variable ‘aap_begin’ [-Wunused-variable]
  Vector<INTs> & aap_begin = buf.aap_begin;
                 ^˜˜˜˜˜˜˜˜
cdhit-common.cpp:2539:17: warning: unused variable ‘taap’ [-Wunused-variable]
  Vector<int>  & taap = buf.taap;
                 ^˜˜˜
cdhit-common.cpp:2545:6: warning: unused variable ‘j’ [-Wunused-variable]
  int j, k, j1, len = seq->size;
      ^
cdhit-common.cpp:2579:6: warning: unused variable ‘M’ [-Wunused-variable]
  int M = frag_size ? table.frag_count : S;
      ^
cdhit-common.cpp:2589:6: warning: unused variable ‘best1’ [-Wunused-variable]
  int best1, sum;
      ^˜˜˜˜
cdhit-common.cpp:2590:8: warning: unused variable ‘lookptr’ [-Wunused-variable]
  INTs *lookptr;
        ^˜˜˜˜˜˜
cdhit-common.cpp: In member function ‘int SequenceDB::CheckOneEST(Sequence*, WordTable&, WorkingParam&, WorkingBuffer&, const Options&)’:
cdhit-common.cpp:2699:17: warning: unused variable ‘aap_list’ [-Wunused-variable]
  Vector<INTs> & aap_list = buf.aap_list;
                 ^˜˜˜˜˜˜˜
cdhit-common.cpp:2700:17: warning: unused variable ‘aap_begin’ [-Wunused-variable]
  Vector<INTs> & aap_begin = buf.aap_begin;
                 ^˜˜˜˜˜˜˜˜
cdhit-common.cpp:2702:17: warning: unused variable ‘taap’ [-Wunused-variable]
  Vector<int>  & taap = buf.taap;
                 ^˜˜˜
cdhit-common.cpp: In member function ‘void SequenceDB::ComputeDistance(const Options&)’:
cdhit-common.cpp:2876:55: warning: unused variable ‘required_aa1’ [-Wunused-variable]
  int band_width1, band_left, band_center, band_right, required_aa1;
                                                       ^˜˜˜˜˜˜˜˜˜˜˜
cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(const Options&, std::__cxx11::string, bool)’:
cdhit-common.cpp:3024:9: warning: unused variable ‘p0’ [-Wunused-variable]
   float p0 = 0;
         ^˜
cdhit-common.cpp:2949:6: warning: unused variable ‘len’ [-Wunused-variable]
  int len, len_bound;
      ^˜˜
cdhit-common.cpp:2949:11: warning: unused variable ‘len_bound’ [-Wunused-variable]
  int len, len_bound;
           ^˜˜˜˜˜˜˜˜
cdhit-common.cpp:2950:6: warning: unused variable ‘flag’ [-Wunused-variable]
  int flag;
      ^˜˜˜
cdhit-common.cpp:2978:9: warning: unused variable ‘mem_limit’ [-Wunused-variable]
  size_t mem_limit = MemoryLimit( mem_need, options );
         ^˜˜˜˜˜˜˜˜
cdhit-common.cpp:2979:9: warning: unused variable ‘mem’ [-Wunused-variable]
  size_t mem, mega = 1000000;
         ^˜˜
cdhit-common.cpp:2979:14: warning: unused variable ‘mega’ [-Wunused-variable]
  size_t mem, mega = 1000000;
              ^˜˜˜
cdhit-common.cpp: In member function ‘void SequenceDB::ClusterTo(SequenceDB&, const Options&)’:
cdhit-common.cpp:3145:11: warning: unused variable ‘seqi’ [-Wunused-variable]
     char *seqi = seq->data;
           ^˜˜˜
cdhit-common.cpp:3063:9: warning: unused variable ‘is’ [-Wunused-variable]
  int i, is, js, flag;
         ^˜
cdhit-common.cpp:3063:13: warning: unused variable ‘js’ [-Wunused-variable]
  int i, is, js, flag;
             ^˜
cdhit-common.cpp:3097:9: warning: unused variable ‘mem_limit’ [-Wunused-variable]
  size_t mem_limit = MemoryLimit( mem_need, options );
         ^˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:488:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c fastaFunctions.cpp -o fastaFunctions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c fmf-common.cpp -o fmf-common.o
fmf-common.cpp: In function ‘Rcpp::List createPanMatrix(Rcpp::IntegerVector, Rcpp::IntegerVector)’:
fmf-common.cpp:24:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < geneRelation.size(); ++i) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c linearKernel.cpp -o linearKernel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c neighborhoodSim.cpp -o neighborhoodSim.o
neighborhoodSim.cpp: In function ‘void filterNeighborhood(std::vector<int>, std::vector<int>, std::vector<int>&)’:
neighborhoodSim.cpp:36:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < neighborhood.size(); i++) {
                     ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
neighborhoodSim.cpp: In function ‘Rcpp::List neighborhoodSim(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::LogicalVector, Rcpp::IntegerVector, double, bool)’:
neighborhoodSim.cpp:113:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (k = 0; k < neighborhoodI.size(); k++) {
                         ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
neighborhoodSim.cpp: In function ‘Rcpp::LogicalVector groupHasParalogues(Rcpp::List, Rcpp::IntegerVector)’:
neighborhoodSim.cpp:443:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (currentOrg < visited.size() && visited[currentOrg]) {
                 ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
neighborhoodSim.cpp:432:9: warning: unused variable ‘maxO’ [-Wunused-variable]
     int maxO = 0;
         ^˜˜˜
neighborhoodSim.cpp: In function ‘Rcpp::DataFrame mergeGroupsByNeighbors(Rcpp::List, Rcpp::DataFrame)’:
neighborhoodSim.cpp:519:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (l = 0; l < lookupMap[group[k]].size(); ++l) {
                             ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c panSim.cpp -o panSim.o
panSim.cpp: In function ‘Rcpp::NumericMatrix panSim(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::CharacterVector)’:
panSim.cpp:16:9: warning: unused variable ‘k’ [-Wunused-variable]
     int k;
         ^
panSim.cpp:19:9: warning: unused variable ‘iVal’ [-Wunused-variable]
     int iVal;
         ^˜˜˜
panSim.cpp:20:9: warning: unused variable ‘jVal’ [-Wunused-variable]
     int jVal;
         ^˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c progress.cpp -o progress.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c smallgraph.cpp -o smallgraph.o
smallgraph.cpp: In member function ‘void Graph::deleteNodes(std::vector<int>)’:
smallgraph.cpp:34:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < ids.size(); ++i) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp:41:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < ids.size(); ++i) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp:53:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = next_possible_edge; i < valid_edge.size(); ++i) {
                                  ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘void Graph::deleteEdges(std::vector<int>)’:
smallgraph.cpp:66:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < ids.size(); ++i) {
                     ˜˜^˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘std::pair<int, int> Graph::firstEdge()’:
smallgraph.cpp:100:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = next_possible_edge; i < valid_edge.size(); ++i) {
                                  ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘std::vector<std::pair<int, int> > Graph::completeTriangle(std::pair<int, int>)’:
smallgraph.cpp:129:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = next_possible_edge; i < valid_edge.size(); ++i) {
                                  ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘bool Graph::isComplete()’:
smallgraph.cpp:145:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itmap->second.size() != maxNeighbors) {
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘std::vector<int> Graph::incidentEdges(int)’:
smallgraph.cpp:166:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = next_possible_edge; i < valid_edge.size(); ++i) {
                                      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘std::vector<int> Graph::edgeIds()’:
smallgraph.cpp:184:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = next_possible_edge; i < valid_edge.size(); ++i) {
                                      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘std::pair<int, int> Graph::getEdge(int)’:
smallgraph.cpp:191:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (id >= valid_edge.size() || !valid_edge[id]) {
         ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp: In member function ‘void Graph::show()’:
smallgraph.cpp:199:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < valid_edge.size(); ++i) {
                     ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp:208:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int k = 0; k < itmap->second.size(); ++k) {
                         ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
smallgraph.cpp:210:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (k != itmap->second.size()-1) Rcout << ", ";
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o FindMyFriends.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o fastaFunctions.o fmf-common.o linearKernel.o neighborhoodSim.o panSim.o progress.o smallgraph.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-FindMyFriends/00new/FindMyFriends/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FindMyFriends)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(FindMyFriends)
> 
> test_check("FindMyFriends")
── 1. Error: kmerLink works (@test-linking.R#9)  ───────────────────────────────
non-numeric argument to binary operator
1: kmerLink(pg, lowerLimit = 0.8, pParam = BiocParallel::SerialParam(), kmerSize = 4) at testthat/test-linking.R:9
2: kmerLink(pg, lowerLimit = 0.8, pParam = BiocParallel::SerialParam(), kmerSize = 4)
3: .local(object, ...)
4: lkParallel(er, pParam, bpworkers(pParam), lowerLimit = lowerLimit)
5: getChunks(nrow(x), nSplits)

── 2. Error: kmerSimilarity works (@test-similarities.R#9)  ────────────────────
non-numeric argument to binary operator
1: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam()) at testthat/test-similarities.R:9
2: kmerSimilarity(pg, lowMem = F, kmerSize = 4, lowerLimit = 0.8, pParam = BiocParallel::SerialParam())
3: .local(object, ...)
4: lkParallel(er, pParam, bpworkers(pParam), lowerLimit = lowerLimit)
5: getChunks(nrow(x), nSplits)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 288 SKIPPED: 1 FAILED: 2
1. Error: kmerLink works (@test-linking.R#9) 
2. Error: kmerSimilarity works (@test-similarities.R#9) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
addGenomes	0.692	0.031	0.799
addGroupInfo	0.104	0.004	0.168
addOrgInfo	0.625	0.012	0.637
cdhitGrouping	3.542	0.280	3.828
collapseParalogues	1.109	0.052	1.182
defaults	0.061	0.024	0.086
fillDefaults	0.004	0.000	0.003
geneLocation	0.272	0.024	0.296
geneNames	0.084	0.000	0.084
geneWidth	0.072	0.012	0.084
genes	0.600	0.008	0.608
getNeighborhood	0.357	0.012	0.369
getRep	0.096	0.008	0.103
gpcGrouping	0.045	0.027	0.072
graphGrouping	0.062	0.000	0.061
groupInfo	0.071	0.004	0.075
groupNames	0.105	0.012	0.116
groupStat	5.991	0.112	6.115
hasGeneGroups	0.121	0.028	0.658
hasGeneInfo	0.319	0.024	0.344
hasParalogueLinks	0.201	0.012	0.214
kmerLink	6.696	0.036	7.188
kmerSimilarity	0.064	0.020	0.084
kmerSplit	0.194	0.004	0.198
loadPgExample	0.893	0.060	1.064
manualGrouping	0.091	0.008	0.100
nGeneGroups	0.072	0.024	0.095
nGenes	0.080	0.004	0.083
nOrganisms	0.072	0.012	0.084
neighborhoodSplit	0.285	0.023	0.308
orgInfo	0.048	0.008	0.057
orgNames	0.054	0.016	0.070
orgStat	0.138	0.008	0.146
pangenome	0.632	0.024	0.656
pcGraph	0.286	0.008	0.294
pgMatrix	0.087	0.004	0.090
plotEvolution	1.054	0.008	1.062
plotGroup	0.273	0.024	0.297
plotNeighborhood	0.346	0.008	0.354
plotSimilarity	1.887	0.032	1.919
plotStat	0.485	0.012	0.497
plotTree	0.466	0.012	0.478
readAnnot	0.640	0.032	1.124
removeGene	0.352	0.004	0.357
reportGroupChanges	0.001	0.000	0.001
seqToGeneGroup	0.084	0.012	0.096
seqToOrg	0.092	0.004	0.096
translated	0.066	0.016	0.083
variableRegions	0.398	0.024	0.423