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CHECK report for FindMyFriends on malbec2

This page was generated on 2018-10-17 08:28:03 -0400 (Wed, 17 Oct 2018).

Package 489/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindMyFriends 1.10.0
Thomas Lin Pedersen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/FindMyFriends
Branch: RELEASE_3_7
Last Commit: 31cae6e
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FindMyFriends
Version: 1.10.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings FindMyFriends_1.10.0.tar.gz
StartedAt: 2018-10-16 00:22:07 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:29:49 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 462.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FindMyFriends.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:FindMyFriends.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings FindMyFriends_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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  8.7Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      5.6Mb
* 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
groupStat 8.684  0.136   8.831
kmerLink  5.544  0.024   5.589
* 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.Rcheck/00check.log’
for details.



Installation output

FindMyFriends.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL FindMyFriends
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘FindMyFriends’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c fastaFunctions.cpp -o fastaFunctions.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c linearKernel.cpp -o linearKernel.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c progress.cpp -o progress.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-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++ -shared -L/home/biocbuild/bbs-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (FindMyFriends)

Tests output

FindMyFriends.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 296 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
300.236  16.360 317.003 

Example timings

FindMyFriends.Rcheck/FindMyFriends-Ex.timings

nameusersystemelapsed
addGenomes0.3600.0240.433
addGroupInfo0.0600.0200.078
addOrgInfo0.0680.0040.071
cdhitGrouping2.8120.1762.993
collapseParalogues0.7880.0160.805
defaults0.0520.0160.069
fillDefaults0.0040.0000.003
geneLocation0.1800.0160.196
geneNames0.0600.0040.066
geneWidth0.0600.0080.068
genes0.3960.0000.394
getNeighborhood0.2440.0160.260
getRep0.1040.0080.111
gpcGrouping0.0480.0120.061
graphGrouping0.0720.0040.078
groupInfo0.0600.0120.069
groupNames0.0560.0080.066
groupStat8.6840.1368.831
hasGeneGroups0.1160.0040.121
hasGeneInfo0.2040.0120.213
hasParalogueLinks0.1280.0240.153
kmerLink5.5440.0245.589
kmerSimilarity0.0480.0120.059
kmerSplit0.0600.0080.067
loadPgExample0.6240.0320.655
manualGrouping0.0520.0160.068
nGeneGroups0.0520.0160.068
nGenes0.0680.0080.077
nOrganisms0.0560.0040.061
neighborhoodSplit0.1600.0080.172
orgInfo0.0600.0040.061
orgNames0.0800.0000.081
orgStat0.1080.0040.109
pangenome0.6640.0120.678
pcGraph0.2960.0080.303
pgMatrix0.0960.0120.107
plotEvolution1.2520.0041.256
plotGroup0.1480.0080.156
plotNeighborhood0.1960.0080.202
plotSimilarity2.3360.0282.368
plotStat0.4560.0280.485
plotTree0.340.000.34
readAnnot0.5440.0240.585
removeGene0.2000.0040.203
reportGroupChanges0.0000.0000.001
seqToGeneGroup0.0560.0120.068
seqToOrg0.0640.0040.068
translated0.0560.0040.062
variableRegions0.2040.0120.218