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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL flowCore
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘flowCore’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c FastLogicle.cpp -o FastLogicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c Hyperlog.cpp -o Hyperlog.o
Hyperlog.cpp: In constructor ‘Hyperlog::IllegalArgument::IllegalArgument(double)’:
Hyperlog.cpp:47:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=]
47 | snprintf(buffer, sizeof(buffer), "Illegal argument value %.17g", value);
| ~~~~~~~~^~~~~~~~~~~~~~~
Hyperlog.cpp:47:38: note: assuming directive output of 23 bytes
47 | snprintf(buffer, sizeof(buffer), "Illegal argument value %.17g", value);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /usr/include/c++/9/cstdio:42,
from /home/biocbuild/bbs-3.16-bioc/R/include/R.h:40,
from zeroin.h:14,
from Hyperlog.cpp:4:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 25 and 48 bytes into a destination of size 8
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Hyperlog.cpp: In constructor ‘Hyperlog::IllegalArgument::IllegalArgument(int)’:
Hyperlog.cpp:53:47: warning: ‘Illegal argument value ’ directive output truncated writing 23 bytes into a region of size 8 [-Wformat-truncation=]
53 | snprintf(buffer, sizeof(buffer), "Illegal argument value %d", value);
| ~~~~~~~~^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /usr/include/c++/9/cstdio:42,
from /home/biocbuild/bbs-3.16-bioc/R/include/R.h:40,
from zeroin.h:14,
from Hyperlog.cpp:4:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 25 and 35 bytes into a destination of size 8
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c Logicle.cpp -o Logicle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c biexponential.cpp -o biexponential.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c convertRawBytes.cpp -o convertRawBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c fcsTextParse.cpp -o fcsTextParse.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 fcsTextParse.cpp:9:
/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 fcsTextParse.cpp:9:
/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 /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/classification.hpp:15,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string/trim.hpp:23,
from /home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include/boost/algorithm/string.hpp:19,
from fcsTextParse.cpp:9:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from fcsTextParse.cpp:13:
/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/site-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-3.16-bioc/R/site-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)
| ~~^~~~~~~~~~~~~~~~~~~~~
fcsTextParse.cpp: In function ‘cpp11::writable::doubles_matrix<> string_to_spill(std::string)’:
fcsTextParse.cpp:21:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
21 | for (auto j = 0; j < spillover.n_cols; j++) {
| ~~^~~~~~~~~~~~~~~~~~
fcsTextParse.cpp:22:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
22 | for (auto i = 0; i < spillover.n_rows; i++) {
| ~~^~~~~~~~~~~~~~~~~~
fcsTextParse.cpp: In function ‘cpp11::sexp fcsTextParse(std::string, bool)’:
fcsTextParse.cpp:142:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
142 | for (int i = 0; i < pairs.size(); i++) {
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c inPolygon.cpp -o inPolygon.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c inPolytope.cpp -o inPolytope.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c logicleTransform.cpp -o logicleTransform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c poly_centroid.cpp -o poly_centroid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c sortBytes.cpp -o sortBytes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c uint2double.cpp -o uint2double.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -c zeroin.cpp -o zeroin.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /home/biocbuild/bbs-3.16-bioc/R/site-library/cytolib/lib/libcytolib.a -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-flowCore/00new/flowCore/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 (flowCore)
