Cannot compile (Fedora 39): make[1]: *** [Makefile:2087: src/essaMEM/sparseSA.lo] Error 1
Closed this issue · 4 comments
MrTomRod commented
I have the following dependencies installed:
- 🐪
v5.38.2 g++ (GCC) 13.2.1 20231205 (Red Hat 13.2.1-6)- not using conda
echo "$CPATH $C_INCLUDE_PATH $CPLUS_INCLUDE_PATH": all variables are unset
What is wrong?
How I try to install:
./configure
mummer-4.0.0rc1$ ./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 commandsmake
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 '<cstdint>'; did you forget to '#include <cstdint>'?
4 | #include "const_iterator_traits.hpp"
+++ |+#include <cstdint>
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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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<IDX>::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<IDX>(p1, p2); }
| ^~
| y1
./include/mummer/48bit_iterator.hpp:149:46: error: 'p2' was not declared in this scope
149 | operator IDX() const { return get<IDX>(p1, p2); }
| ^~
./include/mummer/48bit_iterator.hpp: In member function 'fortyeight_iterator_imp::setter<IDX>& fortyeight_iterator_imp::setter<IDX>::operator=(IDX)':
./include/mummer/48bit_iterator.hpp:151:5: error: 'set' was not declared in this scope; did you mean 'get'?
151 | set<IDX>(p1, p2, x);
| ^~~
| get
./include/mummer/48bit_iterator.hpp:151:12: error: expected primary-expression before '>' token
151 | set<IDX>(p1, p2, x);
| ^
./include/mummer/48bit_iterator.hpp:151:14: error: 'p1' was not declared in this scope; did you mean 'y1'?
151 | set<IDX>(p1, p2, x);
| ^~
| y1
./include/mummer/48bit_iterator.hpp:151:18: error: 'p2' was not declared in this scope
151 | set<IDX>(p1, p2, x);
| ^~
./include/mummer/48bit_iterator.hpp: In member function 'fortyeight_iterator_imp::setter<IDX>::iterator fortyeight_iterator_imp::setter<IDX>::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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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<IDX>::fortyeight_iterator(const fortyeight_iterator<IDX>&)':
./include/mummer/48bit_iterator.hpp:195:57: error: class 'fortyeight_iterator<IDX>' 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<IDX>' 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<IDX>::fortyeight_iterator(std::nullptr_t)':
./include/mummer/48bit_iterator.hpp:196:42: error: class 'fortyeight_iterator<IDX>' 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<IDX>' 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<IDX>::setter_type fortyeight_iterator<IDX>::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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./include/mummer/48bit_iterator.hpp: In constructor 'const_fortyeight_iterator<IDX>::const_fortyeight_iterator(const int*, const int*)':
./include/mummer/48bit_iterator.hpp:220:69: error: class 'const_fortyeight_iterator<IDX>' 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<IDX>' 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<IDX>::const_fortyeight_iterator(const const_fortyeight_iterator<IDX>&)':
./include/mummer/48bit_iterator.hpp:221:69: error: class 'const_fortyeight_iterator<IDX>' 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<IDX>' 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<IDX>::const_fortyeight_iterator(const fortyeight_iterator<IDX>&)':
./include/mummer/48bit_iterator.hpp:222:68: error: class 'const_fortyeight_iterator<IDX>' does not have any field named 'p1'
222 | const_fortyeight_iterator(const fortyeight_iterator<IDX>& rhs) : p1(rhs.p1), p2(rhs.p2) { }
| ^~
./include/mummer/48bit_iterator.hpp:222:80: error: class 'const_fortyeight_iterator<IDX>' does not have any field named 'p2'
222 | const_fortyeight_iterator(const fortyeight_iterator<IDX>& rhs) : p1(rhs.p1), p2(rhs.p2) { }
| ^~
./include/mummer/48bit_iterator.hpp: In constructor 'const_fortyeight_iterator<IDX>::const_fortyeight_iterator(std::nullptr_t)':
./include/mummer/48bit_iterator.hpp:223:48: error: class 'const_fortyeight_iterator<IDX>' 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<IDX>' 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 '<cstdint>'; did you forget to '#include <cstdint>'?
8 | #include "48bit_iterator.hpp"
+++ |+#include <cstdint>
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 '<cstdint>'; did you forget to '#include <cstdint>'?
./include/mummer/48bit_index.hpp: In constructor 'fortyeight_index<IDX>::fortyeight_index()':
./include/mummer/48bit_index.hpp:18:7: error: class 'fortyeight_index<IDX>' does not have any field named 'm_base32'
18 | , m_base32(nullptr)
| ^~~~~~~~
./include/mummer/48bit_index.hpp:19:7: error: class 'fortyeight_index<IDX>' does not have any field named 'm_base16'
19 | , m_base16(nullptr)
| ^~~~~~~~
./include/mummer/48bit_index.hpp: In constructor 'fortyeight_index<IDX>::fortyeight_index(size_t)':
./include/mummer/48bit_index.hpp:23:7: error: class 'fortyeight_index<IDX>' 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 '<cstdint>'; did you forget to '#include <cstdint>'?
./include/mummer/48bit_index.hpp:24:7: error: class 'fortyeight_index<IDX>' 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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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<IDX>::fortyeight_index(fortyeight_index<IDX>&&)':
./include/mummer/48bit_index.hpp:28:7: error: class 'fortyeight_index<IDX>' 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<IDX>' 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<IDX>::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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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 '<cstdint>'; did you forget to '#include <cstdint>'?
./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<IDX>::~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<IDX>::const_iterator fortyeight_index<IDX>::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<IDX>::iterator fortyeight_index<IDX>::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<long int>' 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<long int>' 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<long int>' 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<long int>' 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<IDX>::fortyeight_index(fortyeight_index<IDX>&&) [with IDX = long int]':
./include/mummer/sparseSA.hpp:52:8: required from here
./include/mummer/48bit_index.hpp:32:9: error: 'struct fortyeight_index<long int>' has no member named 'm_base32'
32 | rhs.m_base32 = nullptr;
| ~~~~^~~~~~~~
./include/mummer/48bit_index.hpp:33:9: error: 'struct fortyeight_index<long int>' has no member named 'm_base16'
33 | rhs.m_base16 = nullptr;
| ~~~~^~~~~~~~
./include/mummer/48bit_iterator.hpp: In instantiation of 'IDX fortyeight_iterator_imp::common<Derived, IDX>::operator*() const [with Derived = const_fortyeight_iterator<long int>; IDX = long int]':
./include/mummer/48bit_iterator.hpp:124:12: required from 'IDX fortyeight_iterator_imp::common<Derived, IDX>::operator[](difference_type) const [with Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]'
./include/mummer/48bit_index.hpp:62:51: required from 'IDX fortyeight_index<IDX>::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<long int>' has no member named 'p1'
51 | return get<IDX>(static_cast<const Derived*>(this)->p1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:52:56: error: 'const class const_fortyeight_iterator<long int>' has no member named 'p2'
52 | static_cast<const Derived*>(this)->p2);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common<Derived, IDX>::operator+=(difference_type) [with Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/mummer/48bit_iterator.hpp:108:56: required from 'Derived fortyeight_iterator_imp::common<Derived, IDX>::operator+(difference_type) const [with Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]'
./include/mummer/48bit_iterator.hpp:124:49: required from 'IDX fortyeight_iterator_imp::common<Derived, IDX>::operator[](difference_type) const [with Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]'
./include/mummer/48bit_index.hpp:62:51: required from 'IDX fortyeight_index<IDX>::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<long int>' has no member named 'p1'
103 | self->p1 += n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp:104:11: error: 'class const_fortyeight_iterator<long int>' has no member named 'p2'
104 | self->p2 += n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common<Derived, IDX>::operator<=(const Derived&) const [with Derived = fortyeight_iterator<long int>; IDX = long int]':
./include/compactsufsort/compactsufsort_imp.hpp:224:15: required from 'static void compactsufsort_imp::SA<CHARPTR, SAIDPTR>::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
77 | return static_cast<const Derived*>(this)->p1 <= rhs.p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:77:57: error: 'const class fortyeight_iterator<long int>' has no member named 'p1'
77 | return static_cast<const Derived*>(this)->p1 <= rhs.p1;
| ~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common<Derived, IDX>::operator--() [with Derived = fortyeight_iterator<long int>; IDX = long int]':
./include/compactsufsort/compactsufsort_imp.hpp:225:13: required from 'static void compactsufsort_imp::SA<CHARPTR, SAIDPTR>::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
92 | --self->p1;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp:93:13: error: 'class fortyeight_iterator<long int>' has no member named 'p2'
93 | --self->p2;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common<Derived, IDX>::difference_type fortyeight_iterator_imp::common<Derived, IDX>::operator-(const fortyeight_iterator_imp::common<DD, II>&) const [with DD = fortyeight_iterator<long int>; II = long int; Derived = fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/compactsufsort/compactsufsort_imp.hpp:234:58: required from 'static void compactsufsort_imp::SA<CHARPTR, SAIDPTR>::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
121 | return static_cast<const Derived*>(this)->p1 - static_cast<const DD*>(&rhs)->p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator<long int>' has no member named 'p1'
121 | return static_cast<const Derived*>(this)->p1 - static_cast<const DD*>(&rhs)->p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common<Derived, IDX>::operator<(const Derived&) const [with Derived = fortyeight_iterator<long int>; IDX = long int]':
./include/compactsufsort/compactsufsort_imp.hpp:252:31: required from 'static void compactsufsort_imp::SA<CHARPTR, SAIDPTR>::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
68 | return static_cast<const Derived*>(this)->p1 < rhs.p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:68:56: error: 'const class fortyeight_iterator<long int>' has no member named 'p1'
68 | return static_cast<const Derived*>(this)->p1 < rhs.p1;
| ~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common<Derived, IDX>::operator++() [with Derived = fortyeight_iterator<long int>; IDX = long int]':
./include/compactsufsort/compactsufsort_imp.hpp:252:36: required from 'static void compactsufsort_imp::SA<CHARPTR, SAIDPTR>::construct_SA(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:288:19: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
81 | ++self->p1;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp:82:13: error: 'class fortyeight_iterator<long int>' has no member named 'p2'
82 | ++self->p2;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common<Derived, IDX>::operator+=(difference_type) [with Derived = fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/mummer/48bit_iterator.hpp:108:56: required from 'Derived fortyeight_iterator_imp::common<Derived, IDX>::operator+(difference_type) const [with Derived = fortyeight_iterator<long int>; IDX = long int; difference_type = long int]'
./include/mummer/48bit_iterator.hpp:199:74: required from 'fortyeight_iterator<IDX>::setter_type fortyeight_iterator<IDX>::operator[](difference_type) const [with IDX = long int; setter_type = fortyeight_iterator_imp::setter<long int>; difference_type = long int]'
./include/mummer/48bit_index.hpp:61:75: required from 'decltype (((fortyeight_index<IDX>*)this)->fortyeight_index<IDX>::begin()[i]) fortyeight_index<IDX>::operator[](size_t) [with IDX = long int; decltype (((fortyeight_index<IDX>*)this)->fortyeight_index<IDX>::begin()[i]) = fortyeight_iterator_imp::setter<long int>; 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<long int>' has no member named 'p1'
103 | self->p1 += n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp:104:11: error: 'class fortyeight_iterator<long int>' has no member named 'p2'
104 | self->p2 += n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common<Derived, IDX>::operator-=(difference_type) [with Derived = fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common<Derived, IDX>::operator-(difference_type) const [with Derived = fortyeight_iterator<long int>; IDX = long int; difference_type = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:99:20: required from 'static compactsufsort_imp::SA<CHARPTR, SAIDPTR>::SAIDX compactsufsort_imp::SA<CHARPTR, SAIDPTR>::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
112 | self->p1 -= n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp:113:11: error: 'class fortyeight_iterator<long int>' has no member named 'p2'
113 | self->p2 -= n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common<Derived, IDX>::operator==(const Derived&) const [with Derived = fortyeight_iterator<long int>; IDX = long int]':
./include/compactsufsort/sssort_imp.hpp:595:31: required from 'static void compactsufsort_imp::ss<CHARPTR, SAIDPTR>::swapmerge(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; CSAIDPTR = const_fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/sssort_imp.hpp:654:18: required from 'static void compactsufsort_imp::ss<CHARPTR, SAIDPTR>::sort(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX, SAIDX, saint_t) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; CSAIDPTR = const_fortyeight_iterator<long int>; SAIDX = long int; saint_t = int]'
./include/compactsufsort/compactsufsort_imp.hpp:145:39: required from 'static compactsufsort_imp::SA<CHARPTR, SAIDPTR>::SAIDX compactsufsort_imp::SA<CHARPTR, SAIDPTR>::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
56 | return static_cast<const Derived*>(this)->p1 == rhs.p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:56:57: error: 'const class fortyeight_iterator<long int>' has no member named 'p1'
56 | return static_cast<const Derived*>(this)->p1 == rhs.p1;
| ~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common<Derived, IDX>::difference_type fortyeight_iterator_imp::common<Derived, IDX>::operator-(const fortyeight_iterator_imp::common<DD, II>&) const [with DD = fortyeight_iterator<long int>; II = long int; Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/compactsufsort/trsort_imp.hpp:254:29: required from 'static void compactsufsort_imp::tr<SAIDPTR>::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator<long int>; CSAIDPTR = const_fortyeight_iterator<long int>]'
./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr<SAIDPTR>::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA<CHARPTR, SAIDPTR>::SAIDX compactsufsort_imp::SA<CHARPTR, SAIDPTR>::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
121 | return static_cast<const Derived*>(this)->p1 - static_cast<const DD*>(&rhs)->p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator<long int>' has no member named 'p1'
121 | return static_cast<const Derived*>(this)->p1 - static_cast<const DD*>(&rhs)->p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common<Derived, IDX>::operator-=(difference_type) [with Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common<Derived, IDX>::operator-(difference_type) const [with Derived = const_fortyeight_iterator<long int>; IDX = long int; difference_type = long int]'
./include/compactsufsort/trsort_imp.hpp:264:26: required from 'static void compactsufsort_imp::tr<SAIDPTR>::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator<long int>; CSAIDPTR = const_fortyeight_iterator<long int>]'
./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr<SAIDPTR>::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA<CHARPTR, SAIDPTR>::SAIDX compactsufsort_imp::SA<CHARPTR, SAIDPTR>::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
112 | self->p1 -= n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp:113:11: error: 'class const_fortyeight_iterator<long int>' has no member named 'p2'
113 | self->p2 -= n;
| ~~~~~~^~
./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common<Derived, IDX>::difference_type fortyeight_iterator_imp::common<Derived, IDX>::operator-(const fortyeight_iterator_imp::common<DD, II>&) const [with DD = const_fortyeight_iterator<long int>; II = long int; Derived = fortyeight_iterator<long int>; IDX = long int; difference_type = long int]':
./include/compactsufsort/trsort_imp.hpp:196:11: required from 'static void compactsufsort_imp::tr<SAIDPTR>::copy(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX) [with SAIDPTR = fortyeight_iterator<long int>; CSAIDPTR = const_fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/trsort_imp.hpp:307:17: required from 'static void compactsufsort_imp::tr<SAIDPTR>::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator<long int>; CSAIDPTR = const_fortyeight_iterator<long int>]'
./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr<SAIDPTR>::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA<CHARPTR, SAIDPTR>::SAIDX compactsufsort_imp::SA<CHARPTR, SAIDPTR>::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; SAIDX = long int]'
./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator<long int>; 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<long int>; 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<long int>' has no member named 'p1'
121 | return static_cast<const Derived*>(this)->p1 - static_cast<const DD*>(&rhs)->p1;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
./include/mummer/48bit_iterator.hpp:121:82: error: 'const class const_fortyeight_iterator<long int>' has no member named 'p1'
121 | return static_cast<const Derived*>(this)->p1 - static_cast<const DD*>(&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 2gmarcais commented
I believe that this is an issue with g++ 13. It is fixed in the development branch.
MrTomRod commented
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
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
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