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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL XDE
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘XDE’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Cholesky.cpp -o Cholesky.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Matrix_v2.cpp -o Matrix_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Potential_v2.cpp -o Potential_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Random_v2.cpp -o Random_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8,
from Rinterface_v2.cpp:2:
Random.h:19: warning: "PI" redefined
19 | #define PI 3.14159265
|
In file included from /home/biocbuild/R/R-4.3.0/include/R.h:72,
from Rinterface_v2.cpp:1:
/home/biocbuild/R/R-4.3.0/include/R_ext/Constants.h:39: note: this is the location of the previous definition
39 | #define PI M_PI
|
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Structure.cpp -o Structure.o
Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(int*, int&, int, char**, std::vector<Potential*>&, std::vector<Update*>&, std::vector<Report*>&, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int)’:
Structure.cpp:1971:18: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
1971 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:1983:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
1983 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:1990:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
1990 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:1996:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
1996 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2002:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2002 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2008:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2008 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2014:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2014 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2020:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2020 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2026:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2026 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2032:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2032 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2038:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2038 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2044:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2044 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2050:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2050 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2056:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2056 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2062:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2062 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2068:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2068 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2074:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2074 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2080:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2080 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2086:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2086 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2092:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2092 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2098:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2098 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2104:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2104 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
Structure.cpp:2110:21: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
2110 | filename.empty();
| ~~~~~~~~~~~~~~^~
In file included from /usr/include/c++/10.3.1/string:55,
from Structure.h:4,
from Structure.cpp:5:
/usr/include/c++/10.3.1/bits/basic_string.h:1002:7: note: declared here
1002 | empty() const _GLIBCXX_NOEXCEPT
| ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Update_v2.cpp -o Update_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Utility_v2.cpp -o Utility_v2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
Random.h:19: warning: "PI" redefined
19 | #define PI 3.14159265
|
In file included from /home/biocbuild/R/R-4.3.0/include/R.h:72,
from diffExpressed_main.cpp:4:
/home/biocbuild/R/R-4.3.0/include/R_ext/Constants.h:39: note: this is the location of the previous definition
39 | #define PI M_PI
|
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘qqplot’ in package ‘XDE’
** 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 (XDE)