search

mummer4 / mummer

Mummer alignment tool
Artistic License 2.0
448 stars 107 forks source link

Cannot compile (Fedora 39): make[1]: *** [Makefile:2087: src/essaMEM/sparseSA.lo] Error 1 #204

Closed MrTomRod closed 8 months ago

MrTomRod commented 8 months ago

I have the following dependencies installed:

What is wrong?

How I try to install:

./configure ```bash mummer-4.0.0rc1$ ./configure checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) gcc3 checking for env... /usr/bin/env checking for OpenMP flag of C++ compiler... -fopenmp checking for yaggo... false checking for gnuplot... no checking for gnuplot5... no checking for gnuplot4... no checking for __int128... yes checking if std::thread::sleep_for is supported... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib64/perl5/CORE checking for Perl extension target directory... /usr/local/lib64/perl5/5.38 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fwrapv -fno-strict-aliasing -I/usr/local/include checking for Perl extensions linker flags... -lpthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -L/usr/local/lib -fstack-protector-strong configure: compiling with flags: CXXFLAGS=-DNDEBUG -std=c++0x -g -O2 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating mummer.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands ```
make ```bash mummer-4.0.0rc1$ make make all-am make[1]: Entering directory '/home/username/Downloads/mummer-4.0.0rc1' CXX src/essaMEM/sparseSA.lo In file included from ./include/mummer/48bit_index.hpp:8, from ./include/mummer/sparseSA.hpp:16, from src/essaMEM/sparseSA.cpp:12: ./include/mummer/48bit_iterator.hpp:16:22: error: 'uint32_t' does not name a type 16 | inline IDX get(const uint32_t* p1, const uint16_t* p2) { | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:5:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? 4 | #include "const_iterator_traits.hpp" +++ |+#include 5 | ./include/mummer/48bit_iterator.hpp:16:42: error: 'uint16_t' does not name a type 16 | inline IDX get(const uint32_t* p1, const uint16_t* p2) { | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:16:42: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:25:13: error: variable or field 'set' declared void 25 | inline void set(uint32_t* p1, uint16_t* p2, const IDX x) { | ^~~ ./include/mummer/48bit_iterator.hpp:25:17: error: 'uint32_t' was not declared in this scope 25 | inline void set(uint32_t* p1, uint16_t* p2, const IDX x) { | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:25:17: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:25:27: error: 'p1' was not declared in this scope; did you mean 'y1'? 25 | inline void set(uint32_t* p1, uint16_t* p2, const IDX x) { | ^~ | y1 ./include/mummer/48bit_iterator.hpp:25:31: error: 'uint16_t' was not declared in this scope 25 | inline void set(uint32_t* p1, uint16_t* p2, const IDX x) { | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:25:31: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:25:41: error: 'p2' was not declared in this scope 25 | inline void set(uint32_t* p1, uint16_t* p2, const IDX x) { | ^~ ./include/mummer/48bit_iterator.hpp:25:45: error: expected primary-expression before 'const' 25 | inline void set(uint32_t* p1, uint16_t* p2, const IDX x) { | ^~~~~ ./include/mummer/48bit_iterator.hpp:144:3: error: 'uint32_t' does not name a type 144 | uint32_t* p1; | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:144:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:145:3: error: 'uint16_t' does not name a type 145 | uint16_t* p2; | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:145:3: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:148:18: error: expected ')' before '*' token 148 | setter(uint32_t* x, uint16_t* y) : p1(x), p2(y) { } | ~ ^ | ) ./include/mummer/48bit_iterator.hpp: In member function 'fortyeight_iterator_imp::setter::operator IDX() const': ./include/mummer/48bit_iterator.hpp:149:42: error: 'p1' was not declared in this scope; did you mean 'y1'? 149 | operator IDX() const { return get(p1, p2); } | ^~ | y1 ./include/mummer/48bit_iterator.hpp:149:46: error: 'p2' was not declared in this scope 149 | operator IDX() const { return get(p1, p2); } | ^~ ./include/mummer/48bit_iterator.hpp: In member function 'fortyeight_iterator_imp::setter& fortyeight_iterator_imp::setter::operator=(IDX)': ./include/mummer/48bit_iterator.hpp:151:5: error: 'set' was not declared in this scope; did you mean 'get'? 151 | set(p1, p2, x); | ^~~ | get ./include/mummer/48bit_iterator.hpp:151:12: error: expected primary-expression before '>' token 151 | set(p1, p2, x); | ^ ./include/mummer/48bit_iterator.hpp:151:14: error: 'p1' was not declared in this scope; did you mean 'y1'? 151 | set(p1, p2, x); | ^~ | y1 ./include/mummer/48bit_iterator.hpp:151:18: error: 'p2' was not declared in this scope 151 | set(p1, p2, x); | ^~ ./include/mummer/48bit_iterator.hpp: In member function 'fortyeight_iterator_imp::setter::iterator fortyeight_iterator_imp::setter::operator&()': ./include/mummer/48bit_iterator.hpp:157:42: error: 'p1' was not declared in this scope; did you mean 'y1'? 157 | iterator operator&() { return iterator(p1, p2); } | ^~ | y1 ./include/mummer/48bit_iterator.hpp:157:46: error: 'p2' was not declared in this scope 157 | iterator operator&() { return iterator(p1, p2); } | ^~ ./include/mummer/48bit_iterator.hpp: At global scope: ./include/mummer/48bit_iterator.hpp:186:3: error: 'uint32_t' does not name a type 186 | uint32_t* p1; | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:186:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:187:3: error: 'uint16_t' does not name a type 187 | uint16_t* p2; | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:187:3: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:194:31: error: expected ')' before '*' token 194 | fortyeight_iterator(uint32_t* x, uint16_t* y) : p1(x), p2(y) { } | ~ ^ | ) ./include/mummer/48bit_iterator.hpp: In copy constructor 'fortyeight_iterator::fortyeight_iterator(const fortyeight_iterator&)': ./include/mummer/48bit_iterator.hpp:195:57: error: class 'fortyeight_iterator' does not have any field named 'p1' 195 | fortyeight_iterator(const fortyeight_iterator& rhs) : p1(rhs.p1), p2(rhs.p2) { } | ^~ ./include/mummer/48bit_iterator.hpp:195:69: error: class 'fortyeight_iterator' does not have any field named 'p2' 195 | fortyeight_iterator(const fortyeight_iterator& rhs) : p1(rhs.p1), p2(rhs.p2) { } | ^~ ./include/mummer/48bit_iterator.hpp: In constructor 'fortyeight_iterator::fortyeight_iterator(std::nullptr_t)': ./include/mummer/48bit_iterator.hpp:196:42: error: class 'fortyeight_iterator' does not have any field named 'p1' 196 | fortyeight_iterator(std::nullptr_t ) : p1(nullptr), p2(nullptr) { } | ^~ ./include/mummer/48bit_iterator.hpp:196:55: error: class 'fortyeight_iterator' does not have any field named 'p2' 196 | fortyeight_iterator(std::nullptr_t ) : p1(nullptr), p2(nullptr) { } | ^~ ./include/mummer/48bit_iterator.hpp: In member function 'fortyeight_iterator::setter_type fortyeight_iterator::operator*()': ./include/mummer/48bit_iterator.hpp:198:48: error: 'p1' was not declared in this scope; did you mean 'y1'? 198 | setter_type operator*() { return setter_type(p1, p2); } | ^~ | y1 ./include/mummer/48bit_iterator.hpp:198:52: error: 'p2' was not declared in this scope 198 | setter_type operator*() { return setter_type(p1, p2); } | ^~ ./include/mummer/48bit_iterator.hpp: At global scope: ./include/mummer/48bit_iterator.hpp:208:9: error: 'uint32_t' does not name a type 208 | const uint32_t* p1; | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:208:9: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:209:9: error: 'uint16_t' does not name a type 209 | const uint16_t* p2; | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:209:9: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:220:35: error: 'uint32_t' does not name a type 220 | const_fortyeight_iterator(const uint32_t* x, const uint16_t* y) : p1(x), p2(y) { } | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:220:35: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp:220:54: error: 'uint16_t' does not name a type 220 | const_fortyeight_iterator(const uint32_t* x, const uint16_t* y) : p1(x), p2(y) { } | ^~~~~~~~ ./include/mummer/48bit_iterator.hpp:220:54: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_iterator.hpp: In constructor 'const_fortyeight_iterator::const_fortyeight_iterator(const int*, const int*)': ./include/mummer/48bit_iterator.hpp:220:69: error: class 'const_fortyeight_iterator' does not have any field named 'p1' 220 | const_fortyeight_iterator(const uint32_t* x, const uint16_t* y) : p1(x), p2(y) { } | ^~ ./include/mummer/48bit_iterator.hpp:220:76: error: class 'const_fortyeight_iterator' does not have any field named 'p2' 220 | const_fortyeight_iterator(const uint32_t* x, const uint16_t* y) : p1(x), p2(y) { } | ^~ ./include/mummer/48bit_iterator.hpp: In copy constructor 'const_fortyeight_iterator::const_fortyeight_iterator(const const_fortyeight_iterator&)': ./include/mummer/48bit_iterator.hpp:221:69: error: class 'const_fortyeight_iterator' does not have any field named 'p1' 221 | const_fortyeight_iterator(const const_fortyeight_iterator& rhs) : p1(rhs.p1), p2(rhs.p2) { } | ^~ ./include/mummer/48bit_iterator.hpp:221:81: error: class 'const_fortyeight_iterator' does not have any field named 'p2' 221 | const_fortyeight_iterator(const const_fortyeight_iterator& rhs) : p1(rhs.p1), p2(rhs.p2) { } | ^~ ./include/mummer/48bit_iterator.hpp: In constructor 'const_fortyeight_iterator::const_fortyeight_iterator(const fortyeight_iterator&)': ./include/mummer/48bit_iterator.hpp:222:68: error: class 'const_fortyeight_iterator' does not have any field named 'p1' 222 | const_fortyeight_iterator(const fortyeight_iterator& rhs) : p1(rhs.p1), p2(rhs.p2) { } | ^~ ./include/mummer/48bit_iterator.hpp:222:80: error: class 'const_fortyeight_iterator' does not have any field named 'p2' 222 | const_fortyeight_iterator(const fortyeight_iterator& rhs) : p1(rhs.p1), p2(rhs.p2) { } | ^~ ./include/mummer/48bit_iterator.hpp: In constructor 'const_fortyeight_iterator::const_fortyeight_iterator(std::nullptr_t)': ./include/mummer/48bit_iterator.hpp:223:48: error: class 'const_fortyeight_iterator' does not have any field named 'p1' 223 | const_fortyeight_iterator(std::nullptr_t ) : p1(nullptr), p2(nullptr) { } | ^~ ./include/mummer/48bit_iterator.hpp:223:61: error: class 'const_fortyeight_iterator' does not have any field named 'p2' 223 | const_fortyeight_iterator(std::nullptr_t ) : p1(nullptr), p2(nullptr) { } | ^~ ./include/mummer/48bit_index.hpp: At global scope: ./include/mummer/48bit_index.hpp:13:3: error: 'uint32_t' does not name a type 13 | uint32_t* m_base32; | ^~~~~~~~ ./include/mummer/48bit_index.hpp:9:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? 8 | #include "48bit_iterator.hpp" +++ |+#include 9 | ./include/mummer/48bit_index.hpp:14:3: error: 'uint16_t' does not name a type 14 | uint16_t* m_base16; | ^~~~~~~~ ./include/mummer/48bit_index.hpp:14:3: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_index.hpp: In constructor 'fortyeight_index::fortyeight_index()': ./include/mummer/48bit_index.hpp:18:7: error: class 'fortyeight_index' does not have any field named 'm_base32' 18 | , m_base32(nullptr) | ^~~~~~~~ ./include/mummer/48bit_index.hpp:19:7: error: class 'fortyeight_index' does not have any field named 'm_base16' 19 | , m_base16(nullptr) | ^~~~~~~~ ./include/mummer/48bit_index.hpp: In constructor 'fortyeight_index::fortyeight_index(size_t)': ./include/mummer/48bit_index.hpp:23:7: error: class 'fortyeight_index' does not have any field named 'm_base32' 23 | , m_base32(new uint32_t[(s * 3 + 1) / 2 + 3]) | ^~~~~~~~ ./include/mummer/48bit_index.hpp:23:20: error: 'uint32_t' does not name a type 23 | , m_base32(new uint32_t[(s * 3 + 1) / 2 + 3]) | ^~~~~~~~ ./include/mummer/48bit_index.hpp:23:20: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_index.hpp:24:7: error: class 'fortyeight_index' does not have any field named 'm_base16' 24 | , m_base16((uint16_t*)(m_base32 + s)) | ^~~~~~~~ ./include/mummer/48bit_index.hpp:24:17: error: 'uint16_t' was not declared in this scope 24 | , m_base16((uint16_t*)(m_base32 + s)) | ^~~~~~~~ ./include/mummer/48bit_index.hpp:24:17: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_index.hpp:24:26: error: expected primary-expression before ')' token 24 | , m_base16((uint16_t*)(m_base32 + s)) | ^ ./include/mummer/48bit_index.hpp:24:28: error: 'm_base32' was not declared in this scope 24 | , m_base16((uint16_t*)(m_base32 + s)) | ^~~~~~~~ ./include/mummer/48bit_index.hpp: In constructor 'fortyeight_index::fortyeight_index(fortyeight_index&&)': ./include/mummer/48bit_index.hpp:28:7: error: class 'fortyeight_index' does not have any field named 'm_base32' 28 | , m_base32(rhs.m_base32) | ^~~~~~~~ ./include/mummer/48bit_index.hpp:29:7: error: class 'fortyeight_index' does not have any field named 'm_base16' 29 | , m_base16(rhs.m_base16) | ^~~~~~~~ ./include/mummer/48bit_index.hpp: In member function 'void fortyeight_index::resize(size_t)': ./include/mummer/48bit_index.hpp:39:15: error: 'm_base32' was not declared in this scope 39 | delete [] m_base32; | ^~~~~~~~ ./include/mummer/48bit_index.hpp:41:20: error: 'uint32_t' does not name a type 41 | m_base32 = new uint32_t[(s * 3 + 1) / 2 + 3]; | ^~~~~~~~ ./include/mummer/48bit_index.hpp:41:20: note: 'uint32_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_index.hpp:42:5: error: 'm_base16' was not declared in this scope 42 | m_base16 = (uint16_t*)(m_base32 + s); | ^~~~~~~~ ./include/mummer/48bit_index.hpp:42:17: error: 'uint16_t' was not declared in this scope 42 | m_base16 = (uint16_t*)(m_base32 + s); | ^~~~~~~~ ./include/mummer/48bit_index.hpp:42:17: note: 'uint16_t' is defined in header ''; did you forget to '#include '? ./include/mummer/48bit_index.hpp:42:26: error: expected primary-expression before ')' token 42 | m_base16 = (uint16_t*)(m_base32 + s); | ^ ./include/mummer/48bit_index.hpp: In destructor 'fortyeight_index::~fortyeight_index()': ./include/mummer/48bit_index.hpp:48:15: error: 'm_base32' was not declared in this scope 48 | delete [] m_base32; | ^~~~~~~~ ./include/mummer/48bit_index.hpp: In member function 'fortyeight_index::const_iterator fortyeight_index::begin() const': ./include/mummer/48bit_index.hpp:54:56: error: 'm_base32' was not declared in this scope 54 | const_iterator begin() const { return const_iterator(m_base32, m_base16); } | ^~~~~~~~ ./include/mummer/48bit_index.hpp:54:66: error: 'm_base16' was not declared in this scope 54 | const_iterator begin() const { return const_iterator(m_base32, m_base16); } | ^~~~~~~~ ./include/mummer/48bit_index.hpp: In member function 'fortyeight_index::iterator fortyeight_index::begin()': ./include/mummer/48bit_index.hpp:55:38: error: 'm_base32' was not declared in this scope 55 | iterator begin() { return iterator(m_base32, m_base16); } | ^~~~~~~~ ./include/mummer/48bit_index.hpp:55:48: error: 'm_base16' was not declared in this scope 55 | iterator begin() { return iterator(m_base32, m_base16); } | ^~~~~~~~ src/essaMEM/sparseSA.cpp: In member function 'bool mummer::mummer::vector_32_48::save(std::ostream&&) const': src/essaMEM/sparseSA.cpp:254:33: error: 'const struct fortyeight_index' has no member named 'm_base32' 254 | os.write((const char*)large.m_base32, size * sizeof(uint32_t)); | ^~~~~~~~ src/essaMEM/sparseSA.cpp:255:33: error: 'const struct fortyeight_index' has no member named 'm_base16' 255 | os.write((const char*)large.m_base16, size * sizeof(uint16_t)); | ^~~~~~~~ src/essaMEM/sparseSA.cpp: In member function 'bool mummer::mummer::vector_32_48::load(std::istream&&)': src/essaMEM/sparseSA.cpp:269:26: error: 'struct fortyeight_index' has no member named 'm_base32' 269 | is.read((char*)large.m_base32, size * sizeof(uint32_t)); | ^~~~~~~~ src/essaMEM/sparseSA.cpp:270:26: error: 'struct fortyeight_index' has no member named 'm_base16' 270 | is.read((char*)large.m_base16, size * sizeof(uint16_t)); | ^~~~~~~~ ./include/mummer/48bit_index.hpp: In instantiation of 'fortyeight_index::fortyeight_index(fortyeight_index&&) [with IDX = long int]': ./include/mummer/sparseSA.hpp:52:8: required from here ./include/mummer/48bit_index.hpp:32:9: error: 'struct fortyeight_index' has no member named 'm_base32' 32 | rhs.m_base32 = nullptr; | ~~~~^~~~~~~~ ./include/mummer/48bit_index.hpp:33:9: error: 'struct fortyeight_index' has no member named 'm_base16' 33 | rhs.m_base16 = nullptr; | ~~~~^~~~~~~~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'IDX fortyeight_iterator_imp::common::operator*() const [with Derived = const_fortyeight_iterator; IDX = long int]': ./include/mummer/48bit_iterator.hpp:124:12: required from 'IDX fortyeight_iterator_imp::common::operator[](difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' ./include/mummer/48bit_index.hpp:62:51: required from 'IDX fortyeight_index::operator[](size_t) const [with IDX = long int; size_t = long unsigned int]' ./include/mummer/sparseSA.hpp:67:41: required from here ./include/mummer/48bit_iterator.hpp:51:56: error: 'const class const_fortyeight_iterator' has no member named 'p1' 51 | return get(static_cast(this)->p1, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:52:56: error: 'const class const_fortyeight_iterator' has no member named 'p2' 52 | static_cast(this)->p2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator+=(difference_type) [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/mummer/48bit_iterator.hpp:108:56: required from 'Derived fortyeight_iterator_imp::common::operator+(difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' ./include/mummer/48bit_iterator.hpp:124:49: required from 'IDX fortyeight_iterator_imp::common::operator[](difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' ./include/mummer/48bit_index.hpp:62:51: required from 'IDX fortyeight_index::operator[](size_t) const [with IDX = long int; size_t = long unsigned int]' ./include/mummer/sparseSA.hpp:67:41: required from here ./include/mummer/48bit_iterator.hpp:103:11: error: 'class const_fortyeight_iterator' has no member named 'p1' 103 | self->p1 += n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp:104:11: error: 'class const_fortyeight_iterator' has no member named 'p2' 104 | self->p2 += n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common::operator<=(const Derived&) const [with Derived = fortyeight_iterator; IDX = long int]': ./include/compactsufsort/compactsufsort_imp.hpp:224:15: required from 'static void compactsufsort_imp::SA::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:77:47: error: 'const class fortyeight_iterator' has no member named 'p1' 77 | return static_cast(this)->p1 <= rhs.p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:77:57: error: 'const class fortyeight_iterator' has no member named 'p1' 77 | return static_cast(this)->p1 <= rhs.p1; | ~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator--() [with Derived = fortyeight_iterator; IDX = long int]': ./include/compactsufsort/compactsufsort_imp.hpp:225:13: required from 'static void compactsufsort_imp::SA::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:92:13: error: 'class fortyeight_iterator' has no member named 'p1' 92 | --self->p1; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp:93:13: error: 'class fortyeight_iterator' has no member named 'p2' 93 | --self->p2; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = fortyeight_iterator; II = long int; Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/compactsufsort/compactsufsort_imp.hpp:234:58: required from 'static void compactsufsort_imp::SA::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class fortyeight_iterator' has no member named 'p1' 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator' has no member named 'p1' 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common::operator<(const Derived&) const [with Derived = fortyeight_iterator; IDX = long int]': ./include/compactsufsort/compactsufsort_imp.hpp:252:31: required from 'static void compactsufsort_imp::SA::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:68:47: error: 'const class fortyeight_iterator' has no member named 'p1' 68 | return static_cast(this)->p1 < rhs.p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:68:56: error: 'const class fortyeight_iterator' has no member named 'p1' 68 | return static_cast(this)->p1 < rhs.p1; | ~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator++() [with Derived = fortyeight_iterator; IDX = long int]': ./include/compactsufsort/compactsufsort_imp.hpp:252:36: required from 'static void compactsufsort_imp::SA::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:81:13: error: 'class fortyeight_iterator' has no member named 'p1' 81 | ++self->p1; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp:82:13: error: 'class fortyeight_iterator' has no member named 'p2' 82 | ++self->p2; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator+=(difference_type) [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/mummer/48bit_iterator.hpp:108:56: required from 'Derived fortyeight_iterator_imp::common::operator+(difference_type) const [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]' ./include/mummer/48bit_iterator.hpp:199:74: required from 'fortyeight_iterator::setter_type fortyeight_iterator::operator[](difference_type) const [with IDX = long int; setter_type = fortyeight_iterator_imp::setter; difference_type = long int]' ./include/mummer/48bit_index.hpp:61:75: required from 'decltype (((fortyeight_index*)this)->fortyeight_index::begin()[i]) fortyeight_index::operator[](size_t) [with IDX = long int; decltype (((fortyeight_index*)this)->fortyeight_index::begin()[i]) = fortyeight_iterator_imp::setter; size_t = long unsigned int]' src/essaMEM/sparseSA.cpp:498:59: required from here ./include/mummer/48bit_iterator.hpp:103:11: error: 'class fortyeight_iterator' has no member named 'p1' 103 | self->p1 += n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp:104:11: error: 'class fortyeight_iterator' has no member named 'p2' 104 | self->p2 += n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:99:20: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:112:11: error: 'class fortyeight_iterator' has no member named 'p1' 112 | self->p1 -= n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp:113:11: error: 'class fortyeight_iterator' has no member named 'p2' 113 | self->p2 -= n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common::operator==(const Derived&) const [with Derived = fortyeight_iterator; IDX = long int]': ./include/compactsufsort/sssort_imp.hpp:595:31: required from 'static void compactsufsort_imp::ss::swapmerge(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/sssort_imp.hpp:654:18: required from 'static void compactsufsort_imp::ss::sort(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX, SAIDX, saint_t) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int; saint_t = int]' ./include/compactsufsort/compactsufsort_imp.hpp:145:39: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:56:47: error: 'const class fortyeight_iterator' has no member named 'p1' 56 | return static_cast(this)->p1 == rhs.p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:56:57: error: 'const class fortyeight_iterator' has no member named 'p1' 56 | return static_cast(this)->p1 == rhs.p1; | ~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = fortyeight_iterator; II = long int; Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/compactsufsort/trsort_imp.hpp:254:29: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class const_fortyeight_iterator' has no member named 'p1' 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator' has no member named 'p1' 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' ./include/compactsufsort/trsort_imp.hpp:264:26: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:112:11: error: 'class const_fortyeight_iterator' has no member named 'p1' 112 | self->p1 -= n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp:113:11: error: 'class const_fortyeight_iterator' has no member named 'p2' 113 | self->p2 -= n; | ~~~~~~^~ ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = const_fortyeight_iterator; II = long int; Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': ./include/compactsufsort/trsort_imp.hpp:196:11: required from 'static void compactsufsort_imp::tr::copy(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/trsort_imp.hpp:307:17: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' src/essaMEM/sparseSA.cpp:496:31: required from here ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class fortyeight_iterator' has no member named 'p1' 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class const_fortyeight_iterator' has no member named 'p1' 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ make[1]: *** [Makefile:2087: src/essaMEM/sparseSA.lo] Error 1 make[1]: Leaving directory '/home/username/Downloads/mummer-4.0.0rc1' make: *** [Makefile:1073: all] Error 2 ```
gmarcais commented 8 months ago

I believe that this is an issue with g++ 13. It is fixed in the development branch.

MrTomRod commented 8 months ago

Thanks for the quick reply! I tried to install like this:

$ git clone https://github.com/mummer4/mummer.git && cd mummer
$ git fetch
$ git checkout -b develop remotes/origin/develop
$ sudo dnf install autoconf automake libtool
$ autoreconf --force --install
$ ./configure
$ make
  YAGGO    src/umd/nucmer_cmdline.hpp
make: *** [Makefile:3002: src/umd/nucmer_cmdline.hpp] Error 1

What's wrong?

gmarcais commented 8 months ago

You are now compiling from the git tree. There is a new dependency compare to the distribution tar ball. Try dnf install yaggo then compile.

MrTomRod commented 8 months ago

I ended up using the gcc 12 docker image. Brief summary:

$ podman run -it --rm \
$    -v $HOME/.local/bin/:$HOME/.local/bin/:z \
$    -v $PWD:/data:z \
$    gcc:12-bookworm bash
(container)$ cd /data/mummer-4.0.0rc1
(container)$ ./configure --prefix=/home/USERNAME/.local
(container)$ make -j 10
(container)$ make install