############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL XDE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘XDE’ ... ** this is package ‘XDE’ version ‘2.53.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Cholesky.cpp -o Cholesky.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Matrix_v2.cpp -o Matrix_v2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Potential_v2.cpp -o Potential_v2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Random_v2.cpp -o Random_v2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Rinterface_v2.cpp -o Rinterface_v2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Structure.cpp -o Structure.o Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(int*, int&, int, char**, std::vector&, std::vector&, std::vector&, 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:1971:25: warning: ignoring return value of ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::empty() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 1971 | filename.empty(); | ~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/13/string:54, from Structure.h:4, from Structure.cpp:5: /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 1983 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 1990 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 1996 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2002 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2008 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2014 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2020 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2026 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2032 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2038 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2044 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2050 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2056 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2062 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2068 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2074 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2080 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2086 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2092 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2098 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2104 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | 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; _Alloc = std::allocator]’, declared with attribute ‘nodiscard’ [-Wunused-result] 2110 | filename.empty(); | ~~~~~~~~~~~~~~^~ /usr/include/c++/13/bits/basic_string.h:1220:7: note: declared here 1220 | empty() const _GLIBCXX_NOEXCEPT | ^~~~~ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Update_v2.cpp -o Update_v2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c Utility_v2.cpp -o Utility_v2.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c diffExpressed_main.cpp -o diffExpressed_main.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/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/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/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)