Jellyfish
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20 hours ago •
gmarcais
gmarcais
Cannot make jellyfish-2.2.7
Hi all,
I try to install jellyfish on my cluster. When I try 2.2.7 I get the following:
Output of:
./configure --prefix=/home/usr9/z41809w/jellytest
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-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... /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... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /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... 1966080
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-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 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 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... yes
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 ld used by gcc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... 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... yes
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
enable_htslib
checking for htslib... no
checking for samtools... no
checking for md5sum... md5sum
checking for yaggo... false
checking for x86 cpuid output... unknown
checking for x86-AVX xgetbv output... unknown
checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x80000000 output... 80000008:0:0:0
checking for x86 cpuid 0x00000001 output... 306e4:22200800:7fbee3ff:bfebfbff
checking for x86 cpuid 0x00000007 output... 0:281:0:0
checking for x86 cpuid 0x80000001 output... 0:0:1:2c000800
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether RDRND is supported by the processor... yes
checking whether RDRND is supported by the processor and OS... yes
checking whether C++ compiler accepts -mrdrnd... yes
checking whether BMI1 is supported by the processor... no
checking whether BMI2 is supported by the processor... no
checking whether ADX is supported by the processor... no
checking whether MPX is supported by the processor... no
checking whether PREFETCHWT1 is supported by the processor... no
checking whether ABM is supported by the processor... no
checking whether MMX is supported by the processor... yes
checking whether MMX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mmmx... yes
checking whether SSE is supported by the processor... yes
checking whether SSE is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse... yes
checking whether SSE2 is supported by the processor... yes
checking whether SSE2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse2... yes
checking whether SSE3 is supported by the processor... yes
checking whether SSE3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse3... yes
checking whether SSSE3 is supported by the processor... yes
checking whether SSSE3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mssse3... yes
checking whether SSE4.1 is supported by the processor... yes
checking whether SSE4.1 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse4.1... yes
checking whether SSE4.2 is supported by the processor... yes
checking whether SSE4.2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse4.2... yes
checking whether SSE4a is supported by the processor... no
checking whether SHA is supported by the processor... no
checking whether AES is supported by the processor... yes
checking whether AES is supported by the processor and OS... yes
checking whether C++ compiler accepts -maes... yes
checking whether AVX is supported by the processor... yes
checking whether AVX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx... yes
checking whether FMA3 is supported by the processor... no
checking whether FMA4 is supported by the processor... no
checking whether XOP is supported by the processor... no
checking whether AVX2 is supported by the processor... no
checking whether AVX512-F is supported by the processor... no
checking whether AVX512-CD is supported by the processor... no
checking whether AVX512-PF is supported by the processor... no
checking whether AVX512-ER is supported by the processor... no
checking whether AVX512-VL is supported by the processor... no
checking whether AVX512-BW is supported by the processor... no
checking whether AVX512-DQ is supported by the processor... no
checking whether AVX512-IFMA is supported by the processor... no
checking whether AVX512-VBMI is supported by the processor... no
checking for __int128... no
checking for std::numeric_limits<__int128>... no
checking for _NSGetExecutablePath... no
checking for execinfo.h... yes
checking for ext/stdio_filebuf.h... yes
checking for siginfo_t.si_int... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/compat.sh
config.status: creating jellyfish-2.0.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Output of:
make
make all-am
make[1]: Entering directory `/home/usr9/z41809w/jellyfish-2.2.7'
CXX lib/rectangular_binary_matrix.lo
CXX lib/mer_dna.lo
CXX lib/storage.lo
CXX lib/allocators_mmap.lo
CXX lib/misc.lo
CXX lib/int128.lo
CXX lib/thread_exec.lo
CXX lib/jsoncpp.lo
CXX lib/time.lo
CXX lib/generator_manager.lo
CXXLD libjellyfish-2.0.la
CXX sub_commands/jellyfish.o
CXX sub_commands/count_main.o
In file included from ./include/jellyfish/stream_manager.hpp:27,
from sub_commands/count_main.cc:40:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In member function 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'void jellyfish::whole_sequence_parser<StreamIterator>::open_next_file(jellyfish::whole_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/whole_sequence_parser.hpp:58: instantiated from 'jellyfish::whole_sequence_parser<StreamIterator>::whole_sequence_parser(uint32_t, uint32_t, uint32_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/count_main.cc:82: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:219: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>& std::unique_ptr<_Tp, _Tp_Deleter>::operator=(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/count_main.cc:42:
./include/jellyfish/whole_sequence_parser.hpp: In member function 'void jellyfish::whole_sequence_parser<StreamIterator>::open_next_file(jellyfish::whole_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]':
./include/jellyfish/whole_sequence_parser.hpp:95: note: synthesized method 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)' first required here
In file included from ./include/jellyfish/stream_manager.hpp:27,
from sub_commands/count_main.cc:40:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In copy constructor 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]'
./include/jellyfish/whole_sequence_parser.hpp:95: instantiated from 'void jellyfish::whole_sequence_parser<StreamIterator>::open_next_file(jellyfish::whole_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/whole_sequence_parser.hpp:58: instantiated from 'jellyfish::whole_sequence_parser<StreamIterator>::whole_sequence_parser(uint32_t, uint32_t, uint32_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/count_main.cc:82: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:214: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>::unique_ptr(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/count_main.cc:40:
./include/jellyfish/stream_manager.hpp: In member function 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]':
./include/jellyfish/stream_manager.hpp:146: note: synthesized method 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)' first required here
make[1]: *** [sub_commands/count_main.o] Error 1
make[1]: Leaving directory `/home/usr9/z41809w/jellyfish-2.2.7'
make: *** [all] Error 2
Interestingly, when I try to make 2.2.6 I can install and run just fine. I am happy to use 2.2.6 and unfortunately I have no clue what the error could be.
Best Regards,
Stefan
I guess it is a case of older compiler/standard library (gcc 4.4.7 I presume). Can you apply this patch to your 2.2.7 source tree to see if it fixes the problem? Within jellyfish-2.2.7, apply the patch with patch -p1 < stream.patch.
Let me know if it works.
I have applied the patch as recommoneded. The output of patch -p1 < stream.patch:
[z41809w@cx01 jellyfish-2.2.7]$ patch -p1 < stream.patch
patching file include/jellyfish/mer_overlap_sequence_parser.hpp
patching file include/jellyfish/whole_sequence_parser.hpp
However, make still fails:
[z41809w@cx01 jellyfish-2.2.7]$ ./configure --prefix /home/usr9/z41809w/jellyfish
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-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... /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... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /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... 1966080
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-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 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 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... yes
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 ld used by gcc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... 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... yes
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
enable_htslib
checking for htslib... no
checking for samtools... no
checking for md5sum... md5sum
checking for yaggo... false
checking for x86 cpuid output... unknown
checking for x86-AVX xgetbv output... unknown
checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x80000000 output... 80000008:0:0:0
checking for x86 cpuid 0x00000001 output... 306e4:2200800:7fbee3ff:bfebfbff
checking for x86 cpuid 0x00000007 output... 0:281:0:0
checking for x86 cpuid 0x80000001 output... 0:0:1:2c000800
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether RDRND is supported by the processor... yes
checking whether RDRND is supported by the processor and OS... yes
checking whether C++ compiler accepts -mrdrnd... yes
checking whether BMI1 is supported by the processor... no
checking whether BMI2 is supported by the processor... no
checking whether ADX is supported by the processor... no
checking whether MPX is supported by the processor... no
checking whether PREFETCHWT1 is supported by the processor... no
checking whether ABM is supported by the processor... no
checking whether MMX is supported by the processor... yes
checking whether MMX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mmmx... yes
checking whether SSE is supported by the processor... yes
checking whether SSE is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse... yes
checking whether SSE2 is supported by the processor... yes
checking whether SSE2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse2... yes
checking whether SSE3 is supported by the processor... yes
checking whether SSE3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse3... yes
checking whether SSSE3 is supported by the processor... yes
checking whether SSSE3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mssse3... yes
checking whether SSE4.1 is supported by the processor... yes
checking whether SSE4.1 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse4.1... yes
checking whether SSE4.2 is supported by the processor... yes
checking whether SSE4.2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse4.2... yes
checking whether SSE4a is supported by the processor... no
checking whether SHA is supported by the processor... no
checking whether AES is supported by the processor... yes
checking whether AES is supported by the processor and OS... yes
checking whether C++ compiler accepts -maes... yes
checking whether AVX is supported by the processor... yes
checking whether AVX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx... yes
checking whether FMA3 is supported by the processor... no
checking whether FMA4 is supported by the processor... no
checking whether XOP is supported by the processor... no
checking whether AVX2 is supported by the processor... no
checking whether AVX512-F is supported by the processor... no
checking whether AVX512-CD is supported by the processor... no
checking whether AVX512-PF is supported by the processor... no
checking whether AVX512-ER is supported by the processor... no
checking whether AVX512-VL is supported by the processor... no
checking whether AVX512-BW is supported by the processor... no
checking whether AVX512-DQ is supported by the processor... no
checking whether AVX512-IFMA is supported by the processor... no
checking whether AVX512-VBMI is supported by the processor... no
checking for __int128... no
checking for std::numeric_limits<__int128>... no
checking for _NSGetExecutablePath... no
checking for execinfo.h... yes
checking for ext/stdio_filebuf.h... yes
checking for siginfo_t.si_int... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/compat.sh
config.status: creating jellyfish-2.0.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
[z41809w@cx01 jellyfish-2.2.7]$ make -j 4
make all-am
make[1]: Entering directory `/home/usr9/z41809w/jellyfish-2.2.7'
CXX lib/rectangular_binary_matrix.lo
CXX lib/mer_dna.lo
CXX lib/storage.lo
CXX lib/allocators_mmap.lo
CXX lib/misc.lo
CXX lib/int128.lo
CXX lib/thread_exec.lo
CXX lib/jsoncpp.lo
CXX lib/time.lo
CXX lib/generator_manager.lo
CXX sub_commands/jellyfish.o
CXX sub_commands/count_main.o
CXX sub_commands/info_main.o
CXX sub_commands/dump_main.o
CXX sub_commands/histo_main.o
CXX sub_commands/stats_main.o
CXX sub_commands/merge_main.o
CXX sub_commands/bc_main.o
CXX sub_commands/query_main.o
In file included from ./include/jellyfish/mer_overlap_sequence_parser.hpp:27,
from sub_commands/bc_main.cc:25:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In member function 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'bool jellyfish::mer_overlap_sequence_parser<StreamIterator>::open_next_file(jellyfish::mer_overlap_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/mer_overlap_sequence_parser.hpp:85: instantiated from 'jellyfish::mer_overlap_sequence_parser<StreamIterator>::mer_overlap_sequence_parser(uint16_t, uint32_t, uint32_t, size_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/bc_main.cc:64: instantiated from 'mer_bloom_counter<PathIterator>::mer_bloom_counter(int, jellyfish::mer_dna_bloom_counter&, PathIterator, PathIterator, PathIterator, PathIterator, uint32_t) [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]'
sub_commands/bc_main.cc:134: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:219: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>& std::unique_ptr<_Tp, _Tp_Deleter>::operator=(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/bc_main.cc:25:
./include/jellyfish/mer_overlap_sequence_parser.hpp: In member function 'bool jellyfish::mer_overlap_sequence_parser<StreamIterator>::open_next_file(jellyfish::mer_overlap_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]':
./include/jellyfish/mer_overlap_sequence_parser.hpp:134: note: synthesized method 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)' first required here
In file included from ./include/jellyfish/mer_overlap_sequence_parser.hpp:27,
from sub_commands/bc_main.cc:25:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In copy constructor 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]'
./include/jellyfish/mer_overlap_sequence_parser.hpp:134: instantiated from 'bool jellyfish::mer_overlap_sequence_parser<StreamIterator>::open_next_file(jellyfish::mer_overlap_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/mer_overlap_sequence_parser.hpp:85: instantiated from 'jellyfish::mer_overlap_sequence_parser<StreamIterator>::mer_overlap_sequence_parser(uint16_t, uint32_t, uint32_t, size_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/bc_main.cc:64: instantiated from 'mer_bloom_counter<PathIterator>::mer_bloom_counter(int, jellyfish::mer_dna_bloom_counter&, PathIterator, PathIterator, PathIterator, PathIterator, uint32_t) [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]'
sub_commands/bc_main.cc:134: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:214: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>::unique_ptr(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/bc_main.cc:27:
./include/jellyfish/stream_manager.hpp: In member function 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]':
./include/jellyfish/stream_manager.hpp:146: note: synthesized method 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)' first required here
make[1]: *** [sub_commands/bc_main.o] Error 1
make[1]: *** Waiting for unfinished jobs....
In file included from ./include/jellyfish/stream_manager.hpp:27,
from sub_commands/query_main.cc:22:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In member function 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'bool jellyfish::mer_overlap_sequence_parser<StreamIterator>::open_next_file(jellyfish::mer_overlap_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/mer_overlap_sequence_parser.hpp:85: instantiated from 'jellyfish::mer_overlap_sequence_parser<StreamIterator>::mer_overlap_sequence_parser(uint16_t, uint32_t, uint32_t, size_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/query_main.cc:48: instantiated from 'void query_from_sequence(PathIterator, PathIterator, const Database&, std::ostream&, bool) [with PathIterator = __gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > >, Database = jellyfish::mer_dna_bloom_counter]'
sub_commands/query_main.cc:105: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:219: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>& std::unique_ptr<_Tp, _Tp_Deleter>::operator=(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/query_main.cc:23:
./include/jellyfish/mer_overlap_sequence_parser.hpp: In member function 'bool jellyfish::mer_overlap_sequence_parser<StreamIterator>::open_next_file(jellyfish::mer_overlap_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > > >]':
./include/jellyfish/mer_overlap_sequence_parser.hpp:134: note: synthesized method 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)' first required here
In file included from ./include/jellyfish/stream_manager.hpp:27,
from sub_commands/query_main.cc:22:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In copy constructor 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > >]'
./include/jellyfish/mer_overlap_sequence_parser.hpp:134: instantiated from 'bool jellyfish::mer_overlap_sequence_parser<StreamIterator>::open_next_file(jellyfish::mer_overlap_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/mer_overlap_sequence_parser.hpp:85: instantiated from 'jellyfish::mer_overlap_sequence_parser<StreamIterator>::mer_overlap_sequence_parser(uint16_t, uint32_t, uint32_t, size_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/query_main.cc:48: instantiated from 'void query_from_sequence(PathIterator, PathIterator, const Database&, std::ostream&, bool) [with PathIterator = __gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > >, Database = jellyfish::mer_dna_bloom_counter]'
sub_commands/query_main.cc:105: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:214: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>::unique_ptr(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/query_main.cc:22:
./include/jellyfish/stream_manager.hpp: In member function 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char**, std::vector<const char*, std::allocator<const char*> > >]':
./include/jellyfish/stream_manager.hpp:146: note: synthesized method 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)' first required here
make[1]: *** [sub_commands/query_main.o] Error 1
In file included from ./include/jellyfish/stream_manager.hpp:27,
from sub_commands/count_main.cc:40:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In member function 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'void jellyfish::whole_sequence_parser<StreamIterator>::open_next_file(jellyfish::whole_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/whole_sequence_parser.hpp:58: instantiated from 'jellyfish::whole_sequence_parser<StreamIterator>::whole_sequence_parser(uint32_t, uint32_t, uint32_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/count_main.cc:82: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:219: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>& std::unique_ptr<_Tp, _Tp_Deleter>::operator=(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/count_main.cc:42:
./include/jellyfish/whole_sequence_parser.hpp: In member function 'void jellyfish::whole_sequence_parser<StreamIterator>::open_next_file(jellyfish::whole_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]':
./include/jellyfish/whole_sequence_parser.hpp:95: note: synthesized method 'jellyfish::stream_type& jellyfish::stream_type::operator=(const jellyfish::stream_type&)' first required here
In file included from ./include/jellyfish/stream_manager.hpp:27,
from sub_commands/count_main.cc:40:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In copy constructor 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)':
./include/jellyfish/parser_common.hpp:37: instantiated from 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]'
./include/jellyfish/whole_sequence_parser.hpp:95: instantiated from 'void jellyfish::whole_sequence_parser<StreamIterator>::open_next_file(jellyfish::whole_sequence_parser<StreamIterator>::stream_status&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
./include/jellyfish/whole_sequence_parser.hpp:58: instantiated from 'jellyfish::whole_sequence_parser<StreamIterator>::whole_sequence_parser(uint32_t, uint32_t, uint32_t, StreamIterator&) [with StreamIterator = jellyfish::stream_manager<__gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > > >]'
sub_commands/count_main.cc:82: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:214: error: deleted function 'std::unique_ptr<_Tp, _Tp_Deleter>::unique_ptr(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = std::basic_istream<char, std::char_traits<char> >, _Tp_Deleter = std::default_delete<std::basic_istream<char, std::char_traits<char> > >]'
./include/jellyfish/parser_common.hpp:37: error: used here
In file included from sub_commands/count_main.cc:40:
./include/jellyfish/stream_manager.hpp: In member function 'jellyfish::stream_type jellyfish::stream_manager<PathIterator>::next() [with PathIterator = __gnu_cxx::__normal_iterator<const char* const*, std::vector<const char*, std::allocator<const char*> > >]':
./include/jellyfish/stream_manager.hpp:146: note: synthesized method 'jellyfish::stream_type::stream_type(const jellyfish::stream_type&)' first required here
make[1]: *** [sub_commands/count_main.o] Error 1
make[1]: Leaving directory `/home/usr9/z41809w/jellyfish-2.2.7'
make: *** [all] Error 2
For completeness:
[z41809w@cx01 jellyfish-2.2.7]$ gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
I came just by luck across this and wanted to test ... I could reproduce the same issue with gcc-4.4.7 on Linux and:
-
the patch as download did not even apply for me (probably its format is not respected by my GNU patch)
-
I manually edited the files, made a new patch ( jellyfish-2.2.7-stream.patch.txt ), confirmed it gets applied but still, the error persists
You can run a diff on the two files to see the patch was applied and errors are exactly same: 2.2.7-vanilla.build.log.txt
Anyway, is not an issue with newer gcc and gcc-4.4.7 cannot be used anyway for jellyfish-2.2.9, so what?
