Tim Daniel Rose
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/mosbi |
| git_branch: RELEASE_3_16 |
| git_last_commit: 5f88068 |
| git_last_commit_date: 2022-11-01 11:26:01 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:41 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1251/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mosbi 1.4.0 (landing page) Tim Daniel Rose
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: mosbi |
| Version: 1.4.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mosbi.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings mosbi_1.4.0.tar.gz |
| StartedAt: 2023-04-11 03:35:01 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 03:36:07 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 66.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mosbi.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mosbi.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings mosbi_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/mosbi.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'mosbi/DESCRIPTION' ... OK * this is package 'mosbi' version '1.4.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking 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 'F:/biocbuild/bbs-3.16-bioc/R/library/mosbi/libs/x64/mosbi.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 'F:/biocbuild/bbs-3.16-bioc/meat/mosbi.Rcheck/00check.log' for details.
mosbi.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL mosbi
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'mosbi' ...
** using staged installation
** libs
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attr_graph.cpp -o attr_graph.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attributeConnector.cpp -o attributeConnector.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c attribute_overlap.cpp -o attribute_overlap.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bicluster_methods.cpp -o bicluster_methods.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_graph.cpp -o boost_graph.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-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]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
F:/biocbuild/bbs-3.16-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>&&)':
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/function3.hpp:11,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
from boost_graph.cpp:3:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost_write.cpp -o boost_write.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graph_traits.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-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]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
F:/biocbuild/bbs-3.16-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>&&)':
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/function_template.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/maybe_include.hpp:36,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/function3.hpp:11,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graphviz.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/graphml.hpp:20,
from boost_write.cpp:3:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/container_hash/hash.hpp:47,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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]
244 | for(int i=begin;i<end;i++){
| ~^~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include/RcppParallel/TinyThread.h:7,
from F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include/RcppParallel.h:6,
from distance_matrix.cpp:2:
F:/biocbuild/bbs-3.16-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]':
F:/biocbuild/bbs-3.16-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
F:/biocbuild/bbs-3.16-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]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractBF.cpp -o extractBF.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from extractBF.cpp:3:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function.hpp:30,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from extractBF.cpp:3:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27,
from extractBF.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | 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]
92 | for(int i=0; i<results.size();i++){
| ~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractQUBIC2.cpp -o extractQUBIC2.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from extractQUBIC2.cpp:7:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function.hpp:30,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from extractQUBIC2.cpp:7:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include/Rcpp.h:27,
from extractQUBIC2.cpp:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c full_graph.cpp -o full_graph.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c network_edge_strength.cpp -o network_edge_strength.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sample_biclusters.cpp -o sample_biclusters.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DRCPP_PARALLEL_USE_TBB=1 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_matrix.cpp -o write_matrix.o
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 -LF:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-mosbi/00new/mosbi/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mosbi)
mosbi.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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
1.01 0.12 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 | 0.03 | 0.00 | 0.03 | |
| 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 | 0.01 | 0.00 | 0.01 | |
| 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 | 0.02 | 0.00 | 0.02 | |
| 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 | 0.02 | 0.00 | 0.02 | |
| 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 | |