Back to Multiple platform build/check report for BioC 3.13
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-17 15:05:40 -0400 (Fri, 17 Sep 2021).

CHECK results for FindMyFriends on nebbiolo1

To the developers/maintainers of the FindMyFriends package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindMyFriends.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 634/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FindMyFriends 1.22.0  (landing page)
Thomas Lin Pedersen
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/FindMyFriends
git_branch: RELEASE_3_13
git_last_commit: 526b1e4
git_last_commit_date: 2021-05-19 12:15:44 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: FindMyFriends
Version: 1.22.0
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
StartedAt: 2021-09-16 09:50:02 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 09:58:15 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 493.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: FindMyFriends.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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  6.429  0.052   6.480
groupStat 5.588  0.712   6.301
* 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.



Installation output

FindMyFriends.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL FindMyFriends
###
##############################################################################
##############################################################################


* 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)

Tests output

FindMyFriends.Rcheck/tests/testthat.Rout


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)

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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 39 | SKIP 1 | PASS 295 ]
> 
> proc.time()
   user  system elapsed 
299.541  22.787 322.332 

Example timings

FindMyFriends.Rcheck/FindMyFriends-Ex.timings

nameusersystemelapsed
addGenomes0.4860.0080.496
addGroupInfo0.1180.0120.130
addOrgInfo0.0510.0160.067
cdhitGrouping3.3120.5363.851
collapseParalogues0.5940.0730.667
defaults0.0370.0250.063
fillDefaults0.0010.0020.002
geneLocation0.1560.0000.156
geneNames0.0640.0000.064
geneWidth0.0570.0040.061
genes0.3820.0200.402
getNeighborhood0.2810.0120.292
getRep0.1290.0160.146
gpcGrouping0.0530.0080.061
graphGrouping0.0590.0040.064
groupInfo0.0560.0160.072
groupNames0.0620.0080.070
groupStat5.5880.7126.301
hasGeneGroups0.1050.0320.137
hasGeneInfo0.2100.0560.266
hasParalogueLinks0.1340.0240.158
kmerLink6.4290.0526.480
kmerSimilarity0.0590.0040.063
kmerSplit0.1540.0070.162
loadPgExample0.5460.0520.598
manualGrouping0.0650.0040.069
nGeneGroups0.0620.0040.066
nGenes0.0490.0080.057
nOrganisms0.0500.0110.062
neighborhoodSplit0.1560.0000.156
orgInfo0.0840.0000.083
orgNames0.0430.0160.059
orgStat0.0950.0160.111
pangenome0.6070.0270.635
pcGraph0.2720.0160.289
pgMatrix0.1010.0000.101
plotEvolution0.7180.0160.734
plotGroup0.2990.0240.323
plotNeighborhood0.2520.0120.264
plotSimilarity1.8520.2392.094
plotStat0.3850.0080.393
plotTree0.3100.0090.317
readAnnot1.8630.1231.987
removeGene0.1940.0130.206
reportGroupChanges0.0000.0010.001
seqToGeneGroup0.1100.0050.115
seqToOrg0.0720.0000.073
translated0.0550.0090.063
variableRegions0.1640.0000.164