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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:05 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R 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 | ||||
|
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. |
| Package 1203/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mosbi 1.1.6 (landing page) Tim Daniel Rose
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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 |
############################################################################## ############################################################################## ### ### 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.
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
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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(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
mosbi.Rcheck/mosbi-Ex.timings
| name | user | system | elapsed | |
| NoBFBiclusters | 0 | 0 | 0 | |
| algohistogram | 0 | 0 | 0 | |
| apply_threshold-bicluster_net-method | 0 | 0 | 0 | |
| apply_threshold-cooccurrence_net-method | 0 | 0 | 0 | |
| apply_threshold | 0 | 0 | 0 | |
| attr_overlap | 0 | 0 | 0 | |
| attributeConnector | 0 | 0 | 0 | |
| attribute_graph | 0 | 0 | 0 | |
| bicluster-class | 0 | 0 | 0 | |
| bicluster_heatmap-bicluster-matrix-method | 0.01 | 0.00 | 0.02 | |
| bicluster_heatmap | 0 | 0 | 0 | |
| bicluster_net-class | 0 | 0 | 0 | |
| bicluster_net_to_igraph-bicluster_net-method | 0 | 0 | 0 | |
| bicluster_net_to_igraph | 0 | 0 | 0 | |
| bicluster_network | 0 | 0 | 0 | |
| bicluster_to_matrix | 0 | 0 | 0 | |
| check_names | 0 | 0 | 0 | |
| clean_bicluster_list | 0 | 0 | 0 | |
| colhistogram | 0 | 0 | 0 | |
| cooccurrence_net-class | 0 | 0 | 0 | |
| cooccurrence_net_to_igraph-cooccurrence_net-method | 0 | 0 | 0 | |
| cooccurrence_net_to_igraph | 0 | 0 | 0 | |
| cpp_matrix_subsetting | 0 | 0 | 0 | |
| detect_elements | 0 | 0 | 0 | |
| dim-bicluster-method | 0 | 0 | 0 | |
| distance_matrix | 0 | 0 | 0 | |
| ensemble_biclusters | 0 | 0 | 0 | |
| feature_louvain_overlap | 0 | 0 | 0 | |
| feature_network | 0 | 0 | 0 | |
| filter_bicluster_size | 0 | 0 | 0 | |
| filter_biclusters | 0 | 0 | 0 | |
| filter_matrix | 0 | 0 | 0 | |
| filter_subsets | 0 | 0 | 0 | |
| full_graph | 0 | 0 | 0 | |
| getAkmbiclustClusters | 0 | 0 | 0 | |
| getBFCluster | 0 | 0 | 0 | |
| getBicAREbiclusters | 0 | 0 | 0 | |
| getBiclustClusters | 0 | 0 | 0 | |
| getBiclustpyClusters | 0 | 0 | 0 | |
| getFabiaClusters | 0 | 0 | 0 | |
| getIsaClusters | 0 | 0 | 0 | |
| getQUBIC2biclusters | 0 | 0 | 0 | |
| get_adjacency-bicluster_net-method | 0 | 0 | 0 | |
| get_adjacency | 0 | 0 | 0 | |
| get_algorithms | 0 | 0 | 0 | |
| get_bic_net_algorithms-bicluster_net-method | 0 | 0 | 0 | |
| get_bic_net_algorithms | 0 | 0 | 0 | |
| get_biclusters | 0 | 0 | 0 | |
| get_louvain_communities-bicluster_net-method | 0 | 0 | 0 | |
| get_louvain_communities-cooccurrence_net-method | 0 | 0 | 0 | |
| get_louvain_communities | 0 | 0 | 0 | |
| getallBFClusters | 0 | 0 | 0 | |
| has_names | 0 | 0 | 0 | |
| is_subset_or_identical | 0 | 0 | 0 | |
| mouse_data | 0 | 0 | 0 | |
| network_edge_strength | 0 | 0 | 0 | |
| network_edge_strength_float | 0 | 0 | 0 | |
| node_size | 0 | 0 | 0 | |
| occurance_matrix | 0 | 0 | 0 | |
| occurance_table | 0 | 0 | 0 | |
| p_overlap | 0 | 0 | 0 | |
| p_overlap_2d | 0 | 0 | 0 | |
| p_overlap_2d_higher | 0 | 0 | 0 | |
| p_overlap_higher | 0 | 0 | 0 | |
| plot-bicluster_net-missing-method | 0 | 0 | 0 | |
| plot-cooccurrence_net-missing-method | 0 | 0 | 0 | |
| plot_algo_network | 0 | 0 | 0 | |
| plot_piechart_bicluster_network | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| replace_threshold | 0 | 0 | 0 | |
| replace_values | 0 | 0 | 0 | |
| replace_values_float | 0 | 0 | 0 | |
| rowhistogram | 0 | 0 | 0 | |
| run_akmbiclust | 0 | 0 | 0 | |
| run_bimax | 0 | 0 | 0 | |
| run_cc | 0 | 0 | 0 | |
| run_fabia | 0 | 0 | 0 | |
| run_isa | 0 | 0 | 0 | |
| run_plaid | 0 | 0 | 0 | |
| run_qubic | 0 | 0 | 0 | |
| run_quest | 0 | 0 | 0 | |
| run_spectral | 0 | 0 | 0 | |
| run_unibic | 0 | 0 | 0 | |
| run_xmotifs | 0 | 0 | 0 | |
| sample_biclusters | 0 | 0 | 0 | |
| select_biclusters_from_bicluster_network-bicluster_net-list-method | 0 | 0 | 0 | |
| select_biclusters_from_bicluster_network | 0 | 0 | 0 | |
| set_bicluster_names | 0 | 0 | 0 | |
| similarity_matrix | 0 | 0 | 0 | |
| transpose_bicluster | 0 | 0 | 0 | |
| validate_bicluster | 0 | 0 | 0 | |
| write_graphml | 0 | 0 | 0 | |
| write_matrix | 0 | 0 | 0 | |
| zero_subsetting | 0 | 0 | 0 | |