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 11:05:11 -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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:mosbi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings mosbi_1.4.0.tar.gz |
| StartedAt: 2023-04-10 22:06:55 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:07:46 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 51.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mosbi.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:mosbi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings mosbi_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/mosbi.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘mosbi’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 17.5Mb
sub-directories of 1Mb or more:
libs 17.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘get_communities’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘example-workflow.Rmd’ using ‘UTF-8’... OK
‘similarity-metrics-evaluation.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/mosbi.Rcheck/00check.log’
for details.
mosbi.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL mosbi
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘mosbi’ ...
** using staged installation
** libs
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c attr_graph.cpp -o attr_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c attributeConnector.cpp -o attributeConnector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c attribute_overlap.cpp -o attribute_overlap.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c bicluster_methods.cpp -o bicluster_methods.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_graph.cpp -o boost_graph.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/graph_traits.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_graph.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/function_template.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/detail/maybe_include.hpp:36,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/function3.hpp:11,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/graphviz.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/graphml.hpp:20,
from boost_graph.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_graph.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_write.cpp -o boost_write.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/scoped_ptr.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:22,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/graph_traits.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:24,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/property_map.hpp:598,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:27,
from boost_write.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/function_template.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/detail/maybe_include.hpp:36,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/function3.hpp:11,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/property_map/dynamic_property_map.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/graphviz.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/graphml.hpp:20,
from boost_write.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/container_hash/hash.hpp:47,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/functional/hash.hpp:6,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered/unordered_set.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/unordered_set.hpp:17,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/graph/adjacency_list.hpp:20,
from boost_write.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c distance_matrix.cpp -o distance_matrix.o
distance_matrix.cpp: In member function ‘virtual void SimWorker::operator()(std::size_t, std::size_t)’:
distance_matrix.cpp:244:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
244 | for(int i=begin;i<end;i++){
| ~^~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include/RcppParallel.h:6,
from distance_matrix.cpp:2:
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include/RcppParallel/Common.h: In instantiation of ‘int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]’:
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include/RcppParallel.h:57:28: required from ‘void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = SimWorker; std::size_t = long unsigned int]’
distance_matrix.cpp:278:43: required from here
/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractBF.cpp -o extractBF.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
from extractBF.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:23,
from extractBF.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
from extractBF.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
extractBF.cpp: In function ‘Rcpp::S4 getBFCluster(Rcpp::String, int)’:
extractBF.cpp:92:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
92 | for(int i=0; i<results.size();i++){
| ~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractQUBIC2.cpp -o extractQUBIC2.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
from extractQUBIC2.cpp:7:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:23,
from extractQUBIC2.cpp:7:
/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
from extractQUBIC2.cpp:2:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c full_graph.cpp -o full_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c misc.cpp -o misc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c network_edge_strength.cpp -o network_edge_strength.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c sample_biclusters.cpp -o sample_biclusters.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c write_matrix.cpp -o write_matrix.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o mosbi.so RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-mosbi/00new/mosbi/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mosbi)
mosbi.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(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
0.930 0.075 0.989
mosbi.Rcheck/mosbi-Ex.timings
| name | user | system | elapsed | |
| NoBFBiclusters | 0 | 0 | 0 | |
| algohistogram | 0.001 | 0.000 | 0.000 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| attribute_graph | 0 | 0 | 0 | |
| bicluster-class | 0.003 | 0.000 | 0.003 | |
| bicluster_heatmap-bicluster-matrix-method | 0.03 | 0.00 | 0.03 | |
| bicluster_heatmap | 0.006 | 0.000 | 0.007 | |
| bicluster_net-class | 0.001 | 0.000 | 0.001 | |
| bicluster_net_to_igraph-bicluster_net-method | 0 | 0 | 0 | |
| bicluster_net_to_igraph | 0.001 | 0.000 | 0.000 | |
| bicluster_network | 0 | 0 | 0 | |
| bicluster_to_matrix | 0.001 | 0.000 | 0.001 | |
| check_names | 0 | 0 | 0 | |
| clean_bicluster_list | 0.001 | 0.000 | 0.001 | |
| colhistogram | 0.000 | 0.000 | 0.001 | |
| cooccurrence_net-class | 0.001 | 0.000 | 0.001 | |
| cooccurrence_net_to_igraph-cooccurrence_net-method | 0.000 | 0.000 | 0.001 | |
| cooccurrence_net_to_igraph | 0 | 0 | 0 | |
| cpp_matrix_subsetting | 0.000 | 0.000 | 0.001 | |
| detect_elements | 0.000 | 0.001 | 0.001 | |
| dim-bicluster-method | 0.000 | 0.001 | 0.001 | |
| distance_matrix | 0.000 | 0.001 | 0.001 | |
| ensemble_biclusters | 0.000 | 0.000 | 0.001 | |
| feature_louvain_overlap | 0 | 0 | 0 | |
| feature_network | 0 | 0 | 0 | |
| filter_bicluster_size | 0.002 | 0.000 | 0.001 | |
| filter_biclusters | 0.000 | 0.001 | 0.000 | |
| filter_matrix | 0 | 0 | 0 | |
| filter_subsets | 0.000 | 0.001 | 0.002 | |
| full_graph | 0.000 | 0.000 | 0.001 | |
| getAkmbiclustClusters | 0 | 0 | 0 | |
| getBFCluster | 0 | 0 | 0 | |
| getBicAREbiclusters | 0 | 0 | 0 | |
| getBiclustClusters | 0 | 0 | 0 | |
| getBiclustpyClusters | 0 | 0 | 0 | |
| getFabiaClusters | 0.000 | 0.000 | 0.001 | |
| getIsaClusters | 0 | 0 | 0 | |
| getQUBIC2biclusters | 0 | 0 | 0 | |
| get_adjacency-bicluster_net-method | 0 | 0 | 0 | |
| get_adjacency | 0.001 | 0.000 | 0.000 | |
| get_algorithms | 0.001 | 0.000 | 0.000 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| has_names | 0 | 0 | 0 | |
| is_subset_or_identical | 0.000 | 0.000 | 0.001 | |
| mouse_data | 0.000 | 0.000 | 0.001 | |
| network_edge_strength | 0 | 0 | 0 | |
| network_edge_strength_float | 0.000 | 0.001 | 0.000 | |
| node_size | 0 | 0 | 0 | |
| occurance_matrix | 0 | 0 | 0 | |
| occurance_table | 0 | 0 | 0 | |
| p_overlap | 0.001 | 0.000 | 0.000 | |
| p_overlap_2d | 0 | 0 | 0 | |
| p_overlap_2d_higher | 0.001 | 0.000 | 0.000 | |
| p_overlap_higher | 0 | 0 | 0 | |
| plot-bicluster_net-missing-method | 0.001 | 0.000 | 0.000 | |
| plot-cooccurrence_net-missing-method | 0 | 0 | 0 | |
| plot_algo_network | 0 | 0 | 0 | |
| plot_piechart_bicluster_network | 0 | 0 | 0 | |
| randomize_matrix | 0.001 | 0.000 | 0.000 | |
| replace_threshold | 0 | 0 | 0 | |
| replace_values | 0.001 | 0.000 | 0.001 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| run_qubic | 0 | 0 | 0 | |
| run_quest | 0 | 0 | 0 | |
| run_spectral | 0 | 0 | 0 | |
| run_unibic | 0 | 0 | 0 | |
| run_xmotifs | 0.000 | 0.000 | 0.001 | |
| 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 | 0.002 | 0.000 | 0.001 | |
| similarity_matrix | 0.001 | 0.000 | 0.000 | |
| transpose_bicluster | 0.001 | 0.000 | 0.001 | |
| validate_bicluster | 0.001 | 0.000 | 0.000 | |
| write_graphml | 0 | 0 | 0 | |
| write_matrix | 0.001 | 0.000 | 0.001 | |
| zero_subsetting | 0 | 0 | 0 | |