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CHECK report for FindMyFriends on tokay2

This page was generated on 2018-10-17 08:41:07 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FindMyFriends.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings FindMyFriends_1.10.0.tar.gz
StartedAt: 2018-10-17 01:57:50 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:05:36 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 465.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: FindMyFriends.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FindMyFriends.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings FindMyFriends_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'FindMyFriends' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpo1bxmp/R.INSTALL1c507abc5511/FindMyFriends/man/pgLM-class.Rd:20: file link 'fasta.index' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/FindMyFriends/libs/i386/FindMyFriends.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
groupStat 11.85   0.07   11.94
kmerLink   7.44   0.03    7.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
groupStat     11.93   0.13   12.05
kmerLink       6.23   0.04    6.28
cdhitGrouping  4.66   0.37    5.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.Rcheck/00check.log'
for details.

Installation output

FindMyFriends.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/FindMyFriends_1.10.0.tar.gz && rm -rf FindMyFriends.buildbin-libdir && mkdir FindMyFriends.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FindMyFriends.buildbin-libdir FindMyFriends_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL FindMyFriends_1.10.0.zip && rm FindMyFriends_1.10.0.tar.gz FindMyFriends_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1716k  100 1716k    0     0  23.1M      0 --:--:-- --:--:-- --:--:-- 25.0M

install for i386

* installing *source* package 'FindMyFriends' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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::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:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fastaFunctions.cpp -o fastaFunctions.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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) {
                   ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c linearKernel.cpp -o linearKernel.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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) {
                               ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c progress.cpp -o progress.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 << ", ";
                   ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o FindMyFriends.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o fastaFunctions.o fmf-common.o linearKernel.o neighborhoodSim.o panSim.o progress.o smallgraph.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.buildbin-libdir/FindMyFriends/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FindMyFriends'
    finding HTML links ... done
    FindMyFriends-package                   html  
    addGenomes                              html  
    addGroupInfo                            html  
    addOrgInfo                              html  
    cdhitGrouping                           html  
    collapseParalogues                      html  
    defaults                                html  
    fillDefaults                            html  
    geneLocation                            html  
    geneNames                               html  
    geneWidth                               html  
    genes                                   html  
    getNeighborhood                         html  
    getRep                                  html  
    gpcGrouping                             html  
    finding level-2 HTML links ... done

    graphGrouping                           html  
    groupInfo                               html  
    groupNames                              html  
    groupStat                               html  
    hasGeneGroups                           html  
    hasGeneInfo                             html  
    hasParalogueLinks                       html  
    internalGroupGenes                      html  
    internalMergePangenomes                 html  
    internalMetadata                        html  
    kmerLink                                html  
    kmerSimilarity                          html  
    kmerSplit                               html  
    loadPgExample                           html  
    manualGrouping                          html  
    nGeneGroups                             html  
    nGenes                                  html  
    nOrganisms                              html  
    neighborhoodSplit                       html  
    orgInfo                                 html  
    orgNames                                html  
    orgStat                                 html  
    pangenome                               html  
    pcGraph                                 html  
    pgFull-class                            html  
    pgFullLoc-class                         html  
    pgInMem-class                           html  
    pgInMemLoc-class                        html  
    pgLM-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpo1bxmp/R.INSTALL1c507abc5511/FindMyFriends/man/pgLM-class.Rd:20: file link 'fasta.index' in package 'Biostrings' does not exist and so has been treated as a topic
    pgLMLoc-class                           html  
    pgMatrix                                html  
    pgSlim-class                            html  
    pgSlimLoc-class                         html  
    pgVirtual-class                         html  
    pgVirtualLoc-class                      html  
    plotEvolution                           html  
    plotGroup                               html  
    plotNeighborhood                        html  
    plotSimilarity                          html  
    plotStat                                html  
    plotTree                                html  
    readAnnot                               html  
    removeGene                              html  
    reportGroupChanges                      html  
    seqToGeneGroup                          html  
    seqToOrg                                html  
    translated                              html  
    variableRegions                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'FindMyFriends' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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::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:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fastaFunctions.cpp -o fastaFunctions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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) {
                   ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c linearKernel.cpp -o linearKernel.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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) {
                               ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c progress.cpp -o progress.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 << ", ";
                   ^
C:/Rtools/mingw_64/bin/g++ -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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/FindMyFriends.buildbin-libdir/FindMyFriends/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FindMyFriends' as FindMyFriends_1.10.0.zip
* DONE (FindMyFriends)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'FindMyFriends' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

FindMyFriends.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

R is a collaborative project with many contributors.
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: 286 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  75.57    2.06   77.79

FindMyFriends.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

R is a collaborative project with many contributors.
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: 286 SKIPPED: 4 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  91.71    1.32   93.10

Example timings

FindMyFriends.Rcheck/examples_i386/FindMyFriends-Ex.timings

nameusersystemelapsed
addGenomes0.810.051.11
addGroupInfo0.130.020.21
addOrgInfo0.110.010.13
cdhitGrouping4.200.334.58
collapseParalogues0.830.281.14
defaults0.080.020.09
fillDefaults000
geneLocation0.140.010.16
geneNames0.100.000.09
geneWidth0.080.020.09
genes0.390.030.43
getNeighborhood0.200.030.23
getRep0.140.030.17
gpcGrouping0.060.020.08
graphGrouping0.060.010.08
groupInfo0.070.030.09
groupNames0.080.040.11
groupStat11.85 0.0711.94
hasGeneGroups0.160.050.20
hasGeneInfo0.240.060.30
hasParalogueLinks0.150.050.20
kmerLink7.440.037.55
kmerSimilarity0.090.020.11
kmerSplit0.130.010.14
loadPgExample0.790.211.00
manualGrouping0.190.000.19
nGeneGroups0.130.010.14
nGenes0.110.000.11
nOrganisms0.110.020.12
neighborhoodSplit0.210.000.22
orgInfo0.150.010.16
orgNames0.100.020.12
orgStat0.150.030.17
pangenome0.890.050.94
pcGraph0.460.010.48
pgMatrix0.150.000.15
plotEvolution1.310.031.34
plotGroup0.350.070.41
plotNeighborhood0.230.040.28
plotSimilarity3.140.283.42
plotStat0.660.050.71
plotTree0.530.020.54
readAnnot0.500.070.58
removeGene0.390.040.42
reportGroupChanges000
seqToGeneGroup0.110.090.20
seqToOrg0.100.050.16
translated0.140.030.18
variableRegions0.310.000.31

FindMyFriends.Rcheck/examples_x64/FindMyFriends-Ex.timings

nameusersystemelapsed
addGenomes0.490.070.56
addGroupInfo0.100.010.11
addOrgInfo0.060.020.08
cdhitGrouping4.660.375.14
collapseParalogues0.620.190.81
defaults0.080.000.08
fillDefaults000
geneLocation0.120.030.16
geneNames0.070.020.08
geneWidth0.090.000.09
genes0.660.010.67
getNeighborhood0.320.030.36
getRep0.220.050.26
gpcGrouping0.080.050.13
graphGrouping0.080.030.11
groupInfo0.100.030.14
groupNames0.110.030.14
groupStat11.93 0.1312.05
hasGeneGroups0.110.040.15
hasGeneInfo0.150.050.21
hasParalogueLinks0.190.050.26
kmerLink6.230.046.28
kmerSimilarity0.080.030.11
kmerSplit0.170.020.18
loadPgExample0.610.060.68
manualGrouping0.080.010.09
nGeneGroups0.050.040.08
nGenes0.110.010.12
nOrganisms0.110.020.13
neighborhoodSplit0.180.030.22
orgInfo0.050.040.09
orgNames0.090.040.12
orgStat0.130.030.16
pangenome0.560.060.62
pcGraph0.230.030.27
pgMatrix0.060.030.09
plotEvolution0.940.020.96
plotGroup0.210.010.21
plotNeighborhood0.210.000.22
plotSimilarity2.850.082.92
plotStat0.610.030.65
plotTree0.430.030.46
readAnnot0.750.040.79
removeGene0.240.040.28
reportGroupChanges000
seqToGeneGroup0.080.020.09
seqToOrg0.060.010.08
translated0.050.030.08
variableRegions0.140.000.14