Entering edit mode
6.9 years ago
biomagician
▴
410
Hi,
I have downloaded the latest release of mummer from: https://github.com/gmarcais/mummer/releases
I have tried version 4.0 and 3.9 and both fail to install.
I get this:
software cd mummer-4.0.0beta
**➜ mummer-4.0.0beta ./configure**
checking build system type... x86_64-apple-darwin16.6.0
checking host system type... x86_64-apple-darwin16.6.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
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... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
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... 196608
checking how to convert x86_64-apple-darwin16.6.0 file names to x86_64-apple-darwin16.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin16.6.0 file names to toolchain format... func_convert_file_noop
checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/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... no
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 a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
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... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -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 (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.6.0 dyld
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++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -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 (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin16.6.0 dyld
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... unknown
checking for yaggo... false
checking for __int128... yes
checking if std::thread::sleep_for is supported... yes
checking for perl... /usr/local/bin/perl
checking for Perl prefix... /usr/local/Cellar/perl/5.24.1
checking for Perl extension include path... /usr/local/Cellar/perl/5.24.1/lib/perl5/5.24.1/darwin-thread-multi-2level/CORE
checking for Perl extension target directory... /usr/local/Cellar/perl/5.24.1/lib/perl5/site_perl/5.24.1/darwin-thread-multi-2level
checking for Perl extensions C preprocessor flags... -fno-common -DPERL_DARWIN -mmacosx-version-min=10.11 -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include
checking for Perl extensions linker flags... -mmacosx-version-min=10.11 -bundle -undefined dynamic_lookup -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 config.h
config.status: executing depfiles commands
config.status: executing libtool commands
**➜ mummer-4.0.0beta make**
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
CXX src/essaMEM/sparseSA.lo
In file included from src/essaMEM/sparseSA.cpp:15:
In file included from ./include/compactsufsort/compactsufsort.hpp:11:
In file included from ./include/compactsufsort/compactsufsort_imp.hpp:7:
./include/compactsufsort/sssort_imp.hpp:190:28: error: call to 'ilg' is ambiguous
for(ssize = 0, limit = ilg(last - first);;) {
^~~
./include/compactsufsort/sssort_imp.hpp:646:7: note: in instantiation of member function 'compactsufsort_imp::ss<const unsigned char *, int *>::mintrosort' requested
here
mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
^
./include/compactsufsort/compactsufsort_imp.hpp:144:35: note: in instantiation of member function 'compactsufsort_imp::ss<const unsigned char *, int *>::sort'
requested here
ss<CHARPTR, SAIDPTR>::sort(T, PAb, SA + i, SA + j,
^
./include/compactsufsort/compactsufsort_imp.hpp:286:11: note: in instantiation of member function 'compactsufsort_imp::SA<const unsigned char *, int
*>::sort_typeBstar' requested here
m = sort_typeBstar(T, SA, bucket_A.get(), bucket_B.get(), n);
^
./include/compactsufsort/compactsufsort.hpp:26:91: note: in instantiation of member function 'compactsufsort_imp::SA<const unsigned char *, int *>::create' requested
here
create(CHARPTR T, SAIDPTR SA, SAIDX n) { return compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(T, SA, n); }
^
src/essaMEM/sparseSA.cpp:492:25: note: in instantiation of function template specialization 'compactsufsort::create<const unsigned char *, int *, long>' requested
here
compactsufsort::create((const unsigned char*)(S + 0), (int*)SA.small.data(), N);
^
./include/compactsufsort/divsufsort_private.h:100:16: note: candidate function
inline saint_t ilg(int32_t n) {
^
./include/compactsufsort/divsufsort_private.h:110:16: note: candidate function
inline saint_t ilg(int64_t n) {
^
In file included from src/essaMEM/sparseSA.cpp:15:
In file included from ./include/compactsufsort/compactsufsort.hpp:11:
In file included from ./include/compactsufsort/compactsufsort_imp.hpp:8:
./include/compactsufsort/trsort_imp.hpp:258:28: error: call to 'ilg' is ambiguous
for(ssize = 0, limit = ilg(last - first);;) {
^~~
./include/compactsufsort/trsort_imp.hpp:511:13: note: in instantiation of member function 'compactsufsort_imp::tr<int *>::introsort' requested here
introsort(ISA, ISAd, SA, first, last, &budget);
.......
....
./include/compactsufsort/divsufsort_private.h:110:16: note: candidate function
inline saint_t ilg(int64_t n) {
^
In file included from src/essaMEM/sparseSA.cpp:15:
In file included from ./include/compactsufsort/compactsufsort.hpp:11:
In file included from ./include/compactsufsort/compactsufsort_imp.hpp:8:
./include/compactsufsort/trsort_imp.hpp:258:28: error: call to 'ilg' is ambiguous
for(ssize = 0, limit = ilg(last - first);;) {
^~~
./include/compactsufsort/trsort_imp.hpp:511:13: note: in instantiation of member function 'compactsufsort_imp::tr<fortyeight_iterator<long long> >::introsort'
requested here
introsort(ISA, ISAd, SA, first, last, &budget);
^
./include/compactsufsort/compactsufsort_imp.hpp:169:20: note: in instantiation of member function 'compactsufsort_imp::tr<fortyeight_iterator<long long> >::sort'
requested here
tr<SAIDPTR>::sort(ISAb, SA, m, (SAIDX)1);
^
./include/compactsufsort/compactsufsort_imp.hpp:286:11: note: in instantiation of member function 'compactsufsort_imp::SA<const unsigned char *,
fortyeight_iterator<long long> >::sort_typeBstar' requested here
m = sort_typeBstar(T, SA, bucket_A.get(), bucket_B.get(), n);
^
./include/compactsufsort/compactsufsort.hpp:26:91: note: in instantiation of member function 'compactsufsort_imp::SA<const unsigned char *, fortyeight_iterator<long
long> >::create' requested here
create(CHARPTR T, SAIDPTR SA, SAIDX n) { return compactsufsort_imp::SA<CHARPTR, SAIDPTR>::create(T, SA, n); }
^
src/essaMEM/sparseSA.cpp:496:25: note: in instantiation of function template specialization 'compactsufsort::create<const unsigned char *, fortyeight_iterator<long
long>, long>' requested here
compactsufsort::create((const unsigned char*)(S + 0), SA.large.begin(), N);
^
./include/compactsufsort/divsufsort_private.h:100:16: note: candidate function
inline saint_t ilg(int32_t n) {
^
./include/compactsufsort/divsufsort_private.h:110:16: note: candidate function
inline saint_t ilg(int64_t n) {
^
4 errors generated.
make[1]: *** [src/essaMEM/sparseSA.lo] Error 1
make: *** [all] Error 2
Can anybody help me, please?
Best, C.
Maybe you can download the pre-built versions available here: https://sourceforge.net/projects/mummer/files/mummer/3.23/