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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings FindMyFriends_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/FindMyFriends.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.22.0’
* package encoding: UTF-8
* 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 ... WARNING
Found the following significant warnings:
  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]
  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]
  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]
See ‘/home/biocbuild/bbs-3.13-bioc/meat/FindMyFriends.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
* 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:::compare_unit’ ‘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 (user + system) or elapsed time > 5s
           user system elapsed
kmerLink  6.565  0.032   6.598
groupStat 5.600  0.600   6.200
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/FindMyFriends.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL FindMyFriends
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘FindMyFriends’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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:
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 unsigned int’} and ‘const int’ [-Wsign-compare]
  488 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  156 |   #pragma omp critical
      | 
cdhit-common.cpp:170: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  170 |  #pragma omp critical
      | 
cdhit-common.cpp:2407: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 2407 |    #pragma omp parallel for schedule( dynamic, 1 )
      | 
cdhit-common.cpp:2424: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 2424 |    #pragma omp parallel for schedule( dynamic, 1 )
      | 
cdhit-common.cpp:2426: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
 2426 |     #pragma omp flush (stop)
      | 
cdhit-common.cpp:2447: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 2447 |        #pragma omp critical
      | 
cdhit-common.cpp:2456: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
 2456 |        #pragma omp flush (stop)
      | 
cdhit-common.cpp:2481: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 2481 |     #pragma omp parallel for schedule( dynamic, 1 )
      | 
cdhit-common.cpp:3140: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 3140 |    #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 unsigned int’} and ‘const int’ [-Wsign-compare]
  488 |   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]
  341 |  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]
  394 |  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]
  517 |  INTs *bip;
      |        ^~~
cdhit-common.cpp:540:6: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable]
  540 |  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]
  664 |  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]
  866 |    int s1, k0, back;
      |        ^~
cdhit-common.cpp:866:12: warning: unused variable ‘k0’ [-Wunused-variable]
  866 |    int s1, k0, back;
      |            ^~
cdhit-common.cpp:777:6: warning: unused variable ‘jj’ [-Wunused-variable]
  777 |  int jj, kk;
      |      ^~
cdhit-common.cpp:777:10: warning: unused variable ‘kk’ [-Wunused-variable]
  777 |  int jj, kk;
      |          ^~
cdhit-common.cpp:778:6: warning: unused variable ‘iden_no1’ [-Wunused-variable]
  778 |  int iden_no1;
      |      ^~~~~~~~
cdhit-common.cpp:917:14: warning: unused variable ‘letters’ [-Wunused-variable]
  917 |  const char *letters = "acgtnx";
      |              ^~~~~~~
cdhit-common.cpp:918:14: warning: unused variable ‘letters2’ [-Wunused-variable]
  918 |  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]
 1200 |  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]
 1417 |  int S = frag_count ? frag_count : sequences.size();
      |      ^
cdhit-common.cpp:1418:25: warning: unused variable ‘m’ [-Wunused-variable]
 1418 |  int  j, k, j0, j1, k1, m;
      |                         ^
cdhit-common.cpp:1419:6: warning: unused variable ‘ix1’ [-Wunused-variable]
 1419 |  int ix1, ix2, ix3, ix4;
      |      ^~~
cdhit-common.cpp:1419:11: warning: unused variable ‘ix2’ [-Wunused-variable]
 1419 |  int ix1, ix2, ix3, ix4;
      |           ^~~
cdhit-common.cpp:1419:16: warning: unused variable ‘ix3’ [-Wunused-variable]
 1419 |  int ix1, ix2, ix3, ix4;
      |                ^~~
cdhit-common.cpp:1419:21: warning: unused variable ‘ix4’ [-Wunused-variable]
 1419 |  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]
 1469 |  int i;
      |      ^
cdhit-common.cpp: In member function ‘void Sequence::operator+=(const char*)’:
cdhit-common.cpp:1511:6: warning: unused variable ‘i’ [-Wunused-variable]
 1511 |  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]
 1517 |  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]
 1533 |  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]
 1556 |  memcpy( & tmp, this, sizeof( Sequence ) );
      |                                          ^
In file included from cdhit-common.cpp:37:
cdhit-common.h:364:8: note: ‘struct Sequence’ declared here
  364 | 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]
 1558 |  memcpy( & other, & tmp, sizeof( Sequence ) );
      |                                             ^
In file included from cdhit-common.cpp:37:
cdhit-common.h:364:8: note: ‘struct Sequence’ declared here
  364 | 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]
 1559 |  memset( & tmp, 0, sizeof( Sequence ) );
      |                                       ^
In file included from cdhit-common.cpp:37:
cdhit-common.h:364:8: note: ‘struct Sequence’ declared here
  364 | 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]
 1622 |  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 unsigned int’} [-Wsign-compare]
 1765 |   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 unsigned int’} [-Wsign-compare]
 1766 |   if (len < min_len) min_len = len;
      |       ~~~~^~~~~~~~~
cdhit-common.cpp:1755:9: warning: unused variable ‘j’ [-Wunused-variable]
 1755 |  int i, j, k, len;
      |         ^
cdhit-common.cpp:1755:12: warning: unused variable ‘k’ [-Wunused-variable]
 1755 |  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]
 1944 |     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]
 2098 |   int k = len_eff < invd ? len_eff : invd;
      |       ^
cdhit-common.cpp:2103:7: warning: unused variable ‘ks3’ [-Wunused-variable]
 2103 |   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]
 2104 |   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]
 2255 |   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]
 2329 |  int i, j, k;
      |         ^
cdhit-common.cpp:2337:6: warning: unused variable ‘len’ [-Wunused-variable]
 2337 |  int len, len_bound;
      |      ^~~
cdhit-common.cpp:2337:11: warning: unused variable ‘len_bound’ [-Wunused-variable]
 2337 |  int len, len_bound;
      |           ^~~~~~~~~
cdhit-common.cpp:2338:6: warning: unused variable ‘flag’ [-Wunused-variable]
 2338 |  int flag;
      |      ^~~~
cdhit-common.cpp:2365:6: warning: unused variable ‘K’ [-Wunused-variable]
 2365 |  int K = N - 100 * T;
      |      ^
cdhit-common.cpp:2367:9: warning: unused variable ‘mem_limit’ [-Wunused-variable]
 2367 |  size_t mem_limit = MemoryLimit( mem_need, options );
      |         ^~~~~~~~~
cdhit-common.cpp:2368:9: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable]
 2368 |  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]
 2536 |  Vector<INTs> & aap_list = buf.aap_list;
      |                 ^~~~~~~~
cdhit-common.cpp:2537:17: warning: unused variable ‘aap_begin’ [-Wunused-variable]
 2537 |  Vector<INTs> & aap_begin = buf.aap_begin;
      |                 ^~~~~~~~~
cdhit-common.cpp:2539:17: warning: unused variable ‘taap’ [-Wunused-variable]
 2539 |  Vector<int>  & taap = buf.taap;
      |                 ^~~~
cdhit-common.cpp:2545:6: warning: unused variable ‘j’ [-Wunused-variable]
 2545 |  int j, k, j1, len = seq->size;
      |      ^
cdhit-common.cpp:2579:6: warning: unused variable ‘M’ [-Wunused-variable]
 2579 |  int M = frag_size ? table.frag_count : S;
      |      ^
cdhit-common.cpp:2589:6: warning: unused variable ‘best1’ [-Wunused-variable]
 2589 |  int best1, sum;
      |      ^~~~~
cdhit-common.cpp:2590:8: warning: unused variable ‘lookptr’ [-Wunused-variable]
 2590 |  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]
 2699 |  Vector<INTs> & aap_list = buf.aap_list;
      |                 ^~~~~~~~
cdhit-common.cpp:2700:17: warning: unused variable ‘aap_begin’ [-Wunused-variable]
 2700 |  Vector<INTs> & aap_begin = buf.aap_begin;
      |                 ^~~~~~~~~
cdhit-common.cpp:2702:17: warning: unused variable ‘taap’ [-Wunused-variable]
 2702 |  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]
 2876 |  int band_width1, band_left, band_center, band_right, required_aa1;
      |                                                       ^~~~~~~~~~~~
cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(const Options&, std::string, bool)’:
cdhit-common.cpp:3024:9: warning: unused variable ‘p0’ [-Wunused-variable]
 3024 |   float p0 = 0;
      |         ^~
cdhit-common.cpp:2949:6: warning: unused variable ‘len’ [-Wunused-variable]
 2949 |  int len, len_bound;
      |      ^~~
cdhit-common.cpp:2949:11: warning: unused variable ‘len_bound’ [-Wunused-variable]
 2949 |  int len, len_bound;
      |           ^~~~~~~~~
cdhit-common.cpp:2950:6: warning: unused variable ‘flag’ [-Wunused-variable]
 2950 |  int flag;
      |      ^~~~
cdhit-common.cpp:2978:9: warning: unused variable ‘mem_limit’ [-Wunused-variable]
 2978 |  size_t mem_limit = MemoryLimit( mem_need, options );
      |         ^~~~~~~~~
cdhit-common.cpp:2979:9: warning: unused variable ‘mem’ [-Wunused-variable]
 2979 |  size_t mem, mega = 1000000;
      |         ^~~
cdhit-common.cpp:2979:14: warning: unused variable ‘mega’ [-Wunused-variable]
 2979 |  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]
 3145 |     char *seqi = seq->data;
      |           ^~~~
cdhit-common.cpp:3063:9: warning: unused variable ‘is’ [-Wunused-variable]
 3063 |  int i, is, js, flag;
      |         ^~
cdhit-common.cpp:3063:13: warning: unused variable ‘js’ [-Wunused-variable]
 3063 |  int i, is, js, flag;
      |             ^~
cdhit-common.cpp:3097:9: warning: unused variable ‘mem_limit’ [-Wunused-variable]
 3097 |  size_t mem_limit = MemoryLimit( mem_need, options );
      |         ^~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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:
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 unsigned int’} and ‘const int’ [-Wsign-compare]
  488 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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:
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 unsigned int’} and ‘const int’ [-Wsign-compare]
  488 |   if( band > options.band_width ) band = options.band_width;
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fastaFunctions.cpp -o fastaFunctions.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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 of integer expressions of different signedness: ‘int’ and ‘std::deque<std::pair<int, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   24 |     for (i = 0; i < geneRelation.size(); ++i) {
      |                 ~~^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c linearKernel.cpp -o linearKernel.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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 of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   36 |     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 unsigned int’} [-Wsign-compare]
  113 |             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 unsigned int’} [-Wsign-compare]
  443 |             if (currentOrg < visited.size() && visited[currentOrg]) {
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~
neighborhoodSim.cpp:432:9: warning: unused variable ‘maxO’ [-Wunused-variable]
  432 |     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 unsigned int’} [-Wsign-compare]
  519 |                 for (l = 0; l < lookupMap[group[k]].size(); ++l) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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]
   16 |     int k;
      |         ^
panSim.cpp:19:9: warning: unused variable ‘iVal’ [-Wunused-variable]
   19 |     int iVal;
      |         ^~~~
panSim.cpp:20:9: warning: unused variable ‘jVal’ [-Wunused-variable]
   20 |     int jVal;
      |         ^~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progress.cpp -o progress.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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 of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |     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 unsigned int’} [-Wsign-compare]
   41 |     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 unsigned int’} [-Wsign-compare]
   53 |     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 unsigned int’} [-Wsign-compare]
   66 |     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 unsigned int’} [-Wsign-compare]
  100 |     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 unsigned int’} [-Wsign-compare]
  129 |     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 unsigned int’} and ‘int’ [-Wsign-compare]
  145 |         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 unsigned int’} [-Wsign-compare]
  166 |     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 unsigned int’} [-Wsign-compare]
  184 |     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 unsigned int’} [-Wsign-compare]
  191 |     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 unsigned int’} [-Wsign-compare]
  199 |     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 unsigned int’} [-Wsign-compare]
  208 |         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 unsigned int’} [-Wsign-compare]
  210 |             if (k != itmap->second.size()-1) Rcout << ", ";
      |                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(testthat)
> library(FindMyFriends)
> 
> test_check("FindMyFriends")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 39 | SKIP 1 | PASS 295 ]
> 
> proc.time()
   user  system elapsed 
298.263  23.582 321.855