Question: Problem installing mummer
0
gravatar for cristian
2.4 years ago by
cristian230
cristian230 wrote:

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.

nucmer install alignment mummer • 1.2k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 2.4 years ago by cristian230

Maybe you can download the pre-built versions available here: https://sourceforge.net/projects/mummer/files/mummer/3.23/

ADD REPLYlink written 2.3 years ago by Sej Modha4.5k
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