Greg Finak
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/flowWorkspace |
| git_branch: RELEASE_3_13 |
| git_last_commit: 8b26faf |
| git_last_commit_date: 2021-05-19 11:48:41 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:40 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the flowWorkspace package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowWorkspace.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 669/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowWorkspace 4.4.0 (landing page) Greg Finak
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: flowWorkspace |
| Version: 4.4.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL flowWorkspace |
| StartedAt: 2021-10-14 06:14:53 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 06:18:23 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 210.1 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_API.cpp:9:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
from /home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from ../inst/include/flowWorkspace.h:6,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
RcppExports.cpp:629:43: required from here
/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
30 | delete obj;
| ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cytoctxAPI.cpp -o cytoctxAPI.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoctxAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
from /home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytoframeAPI.cpp:9:43: required from here
/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
30 | delete obj;
| ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
from /home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytosetAPI.cpp:38:81: required from here
/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
30 | delete obj;
| ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getDescendants.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getPopStats.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/bbs-3.13-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 /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:29,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from setCounts.cpp:1:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: #pragma message: This header is deprecated. Use <iterator> instead.
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/config/pragma_message.hpp:24:34: note: in definition of macro ‘BOOST_PRAGMA_MESSAGE’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
13 | BOOST_HEADER_DEPRECATED("<iterator>")
| ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /home/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/libcytolib.a /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.13-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** R
** 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 (flowWorkspace)