Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for mosbi on nebbiolo2


To the developers/maintainers of the mosbi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mosbi.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1268/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosbi 1.5.0  (landing page)
Tim Daniel Rose
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/mosbi
git_branch: devel
git_last_commit: 48241c4
git_last_commit_date: 2022-11-01 11:26:01 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: mosbi
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mosbi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings mosbi_1.5.0.tar.gz
StartedAt: 2023-04-12 07:37:53 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 07:38:52 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 59.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mosbi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:mosbi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings mosbi_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/mosbi.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘mosbi/DESCRIPTION’ ... OK
* this is package ‘mosbi’ version ‘1.5.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mosbi’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘get_communities’
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘example-workflow.Rmd’ using ‘UTF-8’... OK
  ‘similarity-metrics-evaluation.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/mosbi.Rcheck/00check.log’
for details.

Installation output

mosbi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL mosbi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘mosbi’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c attr_graph.cpp -o attr_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c attributeConnector.cpp -o attributeConnector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c attribute_overlap.cpp -o attribute_overlap.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bicluster_methods.cpp -o bicluster_methods.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c boost_graph.cpp -o boost_graph.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/graph_traits.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:24,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/function_template.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/detail/maybe_include.hpp:36,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/function3.hpp:11,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/graphviz.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/graphml.hpp:20,
                 from boost_graph.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c boost_write.cpp -o boost_write.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/scoped_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/graph_traits.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:24,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/function_template.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/detail/maybe_include.hpp:36,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/function3.hpp:11,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/graphviz.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/graphml.hpp:20,
                 from boost_write.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c distance_matrix.cpp -o distance_matrix.o
distance_matrix.cpp: In member function ‘virtual void SimWorker::operator()(std::size_t, std::size_t)’:
distance_matrix.cpp:244:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |   for(int i=begin;i<end;i++){
      |                   ~^~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include/RcppParallel/TinyThread.h:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include/RcppParallel.h:6,
                 from distance_matrix.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include/RcppParallel/Common.h: In instantiation of ‘int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include/RcppParallel.h:57:28:   required from ‘void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = SimWorker; std::size_t = long unsigned int]’
distance_matrix.cpp:278:43:   required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
   16 |    if (requestedValue != defaultValue && requestedValue > 0)
      |        ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c extractBF.cpp -o extractBF.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from extractBF.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from extractBF.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from extractBF.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
extractBF.cpp: In function ‘Rcpp::S4 getBFCluster(Rcpp::String, int)’:
extractBF.cpp:92:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   92 |     for(int i=0; i<results.size();i++){
      |                  ~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c extractQUBIC2.cpp -o extractQUBIC2.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
                 from extractQUBIC2.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:23,
                 from extractQUBIC2.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
                 from extractQUBIC2.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c full_graph.cpp -o full_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c network_edge_strength.cpp -o network_edge_strength.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c sample_biclusters.cpp -o sample_biclusters.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c write_matrix.cpp -o write_matrix.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mosbi.so RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-mosbi/00new/mosbi/libs
** R
** data
** 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 (mosbi)

Tests output

mosbi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(testthat)
> library(mosbi)

Attaching package: 'mosbi'

The following object is masked from 'package:testthat':

    has_names

> 
> test_check("mosbi")
6 6
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  1.510   0.107   1.601

Example timings

mosbi.Rcheck/mosbi-Ex.timings

nameusersystemelapsed
NoBFBiclusters000
algohistogram0.0000.0000.001
apply_threshold-bicluster_net-method000
apply_threshold-cooccurrence_net-method0.0000.0000.001
apply_threshold000
attr_overlap000
attributeConnector000
attribute_graph0.0010.0000.000
bicluster-class0.0020.0000.002
bicluster_heatmap-bicluster-matrix-method0.0270.0000.028
bicluster_heatmap0.0060.0000.006
bicluster_net-class0.0020.0000.001
bicluster_net_to_igraph-bicluster_net-method000
bicluster_net_to_igraph000
bicluster_network000
bicluster_to_matrix0.0010.0000.001
check_names0.0010.0000.000
clean_bicluster_list0.0010.0000.001
colhistogram0.0000.0000.001
cooccurrence_net-class0.0010.0000.001
cooccurrence_net_to_igraph-cooccurrence_net-method000
cooccurrence_net_to_igraph000
cpp_matrix_subsetting0.0000.0000.001
detect_elements0.0010.0000.001
dim-bicluster-method0.0010.0000.000
distance_matrix000
ensemble_biclusters0.0000.0010.000
feature_louvain_overlap0.0000.0000.001
feature_network000
filter_bicluster_size0.0000.0010.001
filter_biclusters0.0000.0010.000
filter_matrix000
filter_subsets0.0030.0000.004
full_graph0.0000.0000.001
getAkmbiclustClusters000
getBFCluster000
getBicAREbiclusters000
getBiclustClusters000
getBiclustpyClusters000
getFabiaClusters0.0010.0000.000
getIsaClusters000
getQUBIC2biclusters000
get_adjacency-bicluster_net-method0.0000.0000.001
get_adjacency000
get_algorithms0.0000.0000.001
get_bic_net_algorithms-bicluster_net-method000
get_bic_net_algorithms0.0000.0000.001
get_biclusters000
get_louvain_communities-bicluster_net-method000
get_louvain_communities-cooccurrence_net-method000
get_louvain_communities000
getallBFClusters000
has_names0.0010.0000.000
is_subset_or_identical000
mouse_data0.0000.0000.001
network_edge_strength000
network_edge_strength_float000
node_size000
occurance_matrix0.0010.0000.000
occurance_table000
p_overlap000
p_overlap_2d000
p_overlap_2d_higher000
p_overlap_higher000
plot-bicluster_net-missing-method000
plot-cooccurrence_net-missing-method0.0000.0000.001
plot_algo_network000
plot_piechart_bicluster_network000
randomize_matrix000
replace_threshold0.0000.0000.001
replace_values0.0010.0000.000
replace_values_float000
rowhistogram000
run_akmbiclust000
run_bimax000
run_cc000
run_fabia000
run_isa000
run_plaid000
run_qubic000
run_quest0.0000.0010.000
run_spectral0.0010.0000.000
run_unibic000
run_xmotifs000
sample_biclusters0.0000.0000.001
select_biclusters_from_bicluster_network-bicluster_net-list-method000
select_biclusters_from_bicluster_network000
set_bicluster_names0.0010.0000.001
similarity_matrix0.0010.0000.001
transpose_bicluster0.0010.0000.001
validate_bicluster0.0000.0000.001
write_graphml000
write_matrix000
zero_subsetting000