Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:08:05 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


To the developers/maintainers of the mosbi package:
- Please 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 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 1203/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mosbi 1.1.6  (landing page)
Tim Daniel Rose
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/mosbi
git_branch: master
git_last_commit: 7abece3
git_last_commit_date: 2022-02-09 06:42:06 -0400 (Wed, 09 Feb 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mosbi
Version: 1.1.6
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mosbi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mosbi_1.1.6.tar.gz
StartedAt: 2022-03-17 19:38:36 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:39:43 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 67.4 seconds
RetCode: 0
Status:   OK  
CheckDir: mosbi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mosbi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mosbi_1.1.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mosbi.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mosbi/DESCRIPTION' ... OK
* this is package 'mosbi' version '1.1.6'
* 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 whether package 'mosbi' can be installed ... OK
* checking installed package size ... OK
* 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
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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/mosbi/libs/x64/mosbi.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/mosbi.Rcheck/00check.log'
for details.



Installation output

mosbi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mosbi
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mosbi' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c attr_graph.cpp -o attr_graph.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c attributeConnector.cpp -o attributeConnector.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c attribute_overlap.cpp -o attribute_overlap.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bicluster_methods.cpp -o bicluster_methods.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c boost_graph.cpp -o boost_graph.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_graph.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/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>&&)':
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/function3.hpp:11,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
                 from boost_graph.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_graph.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c boost_write.cpp -o boost_write.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from boost_write.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/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>&&)':
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/function3.hpp:11,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
                 from boost_write.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/extensions.hpp:34,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/container_hash/hash.hpp:766,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
                 from boost_write.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 long unsigned int'} [-Wsign-compare]
   for(int i=begin;i<end;i++){
                   ~^~~~
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include/RcppParallel/TinyThread.h:7,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include/RcppParallel.h:6,
                 from distance_matrix.cpp:2:
D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include/RcppParallel/Common.h: In instantiation of 'int RcppParallel::resolveValue(const char*, T, U) [with T = long long unsigned int; U = int]':
D:/biocbuild/bbs-3.15-bioc/R/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 long unsigned int]'
distance_matrix.cpp:278:43:   required from here
D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'int' [-Wsign-compare]
    if (requestedValue != defaultValue && requestedValue > 0)
        ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c extractBF.cpp -o extractBF.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from extractBF.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from extractBF.cpp:3:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from extractBF.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   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 long unsigned int'} [-Wsign-compare]
     for(int i=0; i<results.size();i++){
                  ~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c extractQUBIC2.cpp -o extractQUBIC2.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from extractQUBIC2.cpp:7:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from extractQUBIC2.cpp:7:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/rtools40/mingw64/include/c++/8.3.0/iomanip:43,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from extractQUBIC2.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c full_graph.cpp -o full_graph.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c network_edge_strength.cpp -o network_edge_strength.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sample_biclusters.cpp -o sample_biclusters.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++17 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c write_matrix.cpp -o write_matrix.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o mosbi.dll tmp.def 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 -LD:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mosbi/00new/mosbi/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mosbi'
    finding HTML links ... done
    NoBFBiclusters                          html  
    algohistogram                           html  
    apply_threshold-bicluster_net-method    html  
    apply_threshold-cooccurrence_net-method
                                            html  
    apply_threshold                         html  
    attr_overlap                            html  
    attributeConnector                      html  
    attribute_graph                         html  
    bicluster-class                         html  
    bicluster_heatmap-bicluster-matrix-method
                                            html  
    bicluster_heatmap                       html  
    bicluster_net-class                     html  
    bicluster_net_to_igraph-bicluster_net-method
                                            html  
    bicluster_net_to_igraph                 html  
    bicluster_network                       html  
    bicluster_to_matrix-matrix-bicluster-method
                                            html  
    bicluster_to_matrix                     html  
    check_names                             html  
    clean_bicluster_list                    html  
    colhistogram                            html  
    cooccurrence_net-class                  html  
    cooccurrence_net_to_igraph-cooccurrence_net-method
                                            html  
    cooccurrence_net_to_igraph              html  
    cpp_matrix_subsetting                   html  
    detect_elements                         html  
    dim-bicluster-method                    html  
    distance_matrix                         html  
    ensemble_biclusters                     html  
    feature_louvain_overlap                 html  
    feature_network                         html  
    filter_bicluster_size                   html  
    filter_biclusters                       html  
    filter_matrix                           html  
    filter_subsets                          html  
    full_graph                              html  
    getAkmbiclustClusters                   html  
    getBFCluster                            html  
    getBicAREbiclusters                     html  
    getBiclustClusters                      html  
    getBiclustpyClusters                    html  
    getFabiaClusters                        html  
    getIsaClusters                          html  
    getQUBIC2biclusters                     html  
    get_adjacency-bicluster_net-method      html  
    get_adjacency                           html  
    get_algorithms                          html  
    get_bic_net_algorithms-bicluster_net-method
                                            html  
    get_bic_net_algorithms                  html  
    get_biclusters                          html  
    get_louvain_communities-bicluster_net-method
                                            html  
    get_louvain_communities-cooccurrence_net-method
                                            html  
    get_louvain_communities                 html  
    getallBFClusters                        html  
    has_names                               html  
    is_subset_or_identical                  html  
    mouse_data                              html  
    network_edge_strength                   html  
    network_edge_strength_float             html  
    node_size                               html  
    occurance_matrix                        html  
    occurance_table                         html  
    p_overlap                               html  
    p_overlap_2d                            html  
    p_overlap_2d_higher                     html  
    p_overlap_higher                        html  
    plot-bicluster_net-missing-method       html  
    plot-cooccurrence_net-missing-method    html  
    plot_algo_network                       html  
    plot_piechart_bicluster_network         html  
    randomize_matrix                        html  
    replace_threshold                       html  
    replace_values                          html  
    replace_values_float                    html  
    rowhistogram                            html  
    run_akmbiclust                          html  
    run_bimax                               html  
    run_cc                                  html  
    run_fabia                               html  
    run_isa                                 html  
    run_plaid                               html  
    run_qubic                               html  
    run_quest                               html  
    run_spectral                            html  
    run_unibic                              html  
    run_xmotifs                             html  
    sample_biclusters                       html  
    select_biclusters_from_bicluster_network-bicluster_net-list-method
                                            html  
    select_biclusters_from_bicluster_network
                                            html  
    set_bicluster_names-bicluster-matrix-method
                                            html  
    set_bicluster_names                     html  
    similarity_matrix                       html  
    transpose_bicluster                     html  
    validate_bicluster                      html  
    write_graphml                           html  
    write_matrix                            html  
    zero_subsetting                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mosbi)
Making 'packages.html' ... done

Tests output

mosbi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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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 
   0.96    0.21    1.17 

Example timings

mosbi.Rcheck/mosbi-Ex.timings

nameusersystemelapsed
NoBFBiclusters000
algohistogram000
apply_threshold-bicluster_net-method000
apply_threshold-cooccurrence_net-method000
apply_threshold000
attr_overlap000
attributeConnector000
attribute_graph000
bicluster-class000
bicluster_heatmap-bicluster-matrix-method0.010.000.02
bicluster_heatmap000
bicluster_net-class000
bicluster_net_to_igraph-bicluster_net-method000
bicluster_net_to_igraph000
bicluster_network000
bicluster_to_matrix000
check_names000
clean_bicluster_list000
colhistogram000
cooccurrence_net-class000
cooccurrence_net_to_igraph-cooccurrence_net-method000
cooccurrence_net_to_igraph000
cpp_matrix_subsetting000
detect_elements000
dim-bicluster-method000
distance_matrix000
ensemble_biclusters000
feature_louvain_overlap000
feature_network000
filter_bicluster_size000
filter_biclusters000
filter_matrix000
filter_subsets000
full_graph000
getAkmbiclustClusters000
getBFCluster000
getBicAREbiclusters000
getBiclustClusters000
getBiclustpyClusters000
getFabiaClusters000
getIsaClusters000
getQUBIC2biclusters000
get_adjacency-bicluster_net-method000
get_adjacency000
get_algorithms000
get_bic_net_algorithms-bicluster_net-method000
get_bic_net_algorithms000
get_biclusters000
get_louvain_communities-bicluster_net-method000
get_louvain_communities-cooccurrence_net-method000
get_louvain_communities000
getallBFClusters000
has_names000
is_subset_or_identical000
mouse_data000
network_edge_strength000
network_edge_strength_float000
node_size000
occurance_matrix000
occurance_table000
p_overlap000
p_overlap_2d000
p_overlap_2d_higher000
p_overlap_higher000
plot-bicluster_net-missing-method000
plot-cooccurrence_net-missing-method000
plot_algo_network000
plot_piechart_bicluster_network000
randomize_matrix000
replace_threshold000
replace_values000
replace_values_float000
rowhistogram000
run_akmbiclust000
run_bimax000
run_cc000
run_fabia000
run_isa000
run_plaid000
run_qubic000
run_quest000
run_spectral000
run_unibic000
run_xmotifs000
sample_biclusters000
select_biclusters_from_bicluster_network-bicluster_net-list-method000
select_biclusters_from_bicluster_network000
set_bicluster_names000
similarity_matrix000
transpose_bicluster000
validate_bicluster000
write_graphml000
write_matrix000
zero_subsetting000