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ekg / edyeet

base-accurate DNA sequence alignments using edlib and mashmap2
MIT License
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About install edyeet! #8

Open sunnycqcn opened 3 years ago

sunnycqcn commented 3 years ago

Hello developer, Happy new year! When I installed the edyeet, I met the error as following: -- Configuring done CMake Warning (dev) at src/common/wflign/deps/edlib/CMakeLists.txt:54 (add_library): Policy CMP0063 is not set: Honor visibility properties for all target types. Run "cmake --help-policy CMP0063" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Target "edlib" of type "STATIC_LIBRARY" has the following visibility properties set for CXX:

CXX_VISIBILITY_PRESET
VISIBILITY_INLINES_HIDDEN

For compatibility CMake is not honoring them for this target. This warning is for project developers. Use -Wno-dev to suppress it. ################################################ If you have some time, could you help me figure out this? Thanks, Fuyou

sunnycqcn commented 3 years ago

Hello developer, I have figured out the problem above. However, I still met the error like this: /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp: In function 'void wflambda::counter_print_stats(FILE*, const wflambda::profiler_counter_t*, const wflambda::profiler_counter_t*, const char*)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:147:33: error: expected ')' before 'PRIu64' 147 | fprintf(stream," (samples=%" PRIu64 "G",num_samples/METRIC_FACTOR_1G); I think this error from your code. I am not sure which I should modified. Thanks, Fuyou

ekg commented 3 years ago

Happy new year! How did you build this?

Let's fix the problem.

Is this happening during install?

On Sat, Jan 2, 2021, 02:51 sunnycqcn notifications@github.com wrote:

Hello developer, I have figured out the problem above. However, I still met the error like this: /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp: In function 'void wflambda::counter_print_stats(FILE, const wflambda::profiler_counter_t, const wflambda::profiler_counter_t, const char)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:147:33: error: expected ')' before 'PRIu64' 147 | fprintf(stream," (samples=%" PRIu64 "G",num_samples/METRIC_FACTOR_1G); I think this error from your code. I am not sure which I should modified. Thanks, Fuyou

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sunnycqcn commented 3 years ago

Yes. It is intalling. Thanks, Fuyou

sunnycqcn commented 3 years ago

Hello, These are all errors when I installed it. It looks like I met the C++ version problem. I used g++ version 9.3 under conda. But I can install well old version (v0.1). Setting warning flags -- Configuring done -- Generating done -- Build files have been written to: /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/build [ 2%] Building CXX object src/common/wflign/deps/edlib/CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o [ 11%] Built target libwflign_static [ 26%] Building CXX object src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/system/profiler_timer.cpp.o [ 26%] Building CXX object src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/edit/edit_cigar.cpp.o [ 26%] Building CXX object src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/edit/edit_table.cpp.o [ 26%] Building CXX object src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/system/mm_allocator.cpp.o [ 26%] Building CXX object src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/system/profiler_counter.cpp.o /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp: In function 'void wflambda::timer_print(FILE*, const wflambda::profiler_timer_t*, const wflambda::profiler_timer_t*)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:125:24: error: expected ')' before 'PRIu64' 125 | fprintf(stream,"%7" PRIu64 " ns",total_time_ns); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:144:26: error: expected ')' before 'PRIu64' 144 | fprintf(stream," (%5" PRIu64 " Gcalls",num_calls/1000000000); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp: In function 'void wflambda::counter_print_stats(FILE*, const wflambda::profiler_counter_t*, const wflambda::profiler_counter_t*, const char*)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:147:33: error: expected ')' before 'PRIu64' 147 | fprintf(stream," (samples=%" PRIu64 "G",num_samples/METRIC_FACTOR_1G); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:146:26: error: expected ')' before 'PRIu64' 146 | fprintf(stream," (%5" PRIu64 " Mcalls",num_calls/1000000); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:149:33: error: expected ')' before 'PRIu64' 149 | fprintf(stream," (samples=%" PRIu64 "M",num_samples/METRIC_FACTOR_1M); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:148:26: error: expected ')' before 'PRIu64' 148 | fprintf(stream," (%5" PRIu64 " Kcalls",num_calls/1000); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:151:33: error: expected ')' before 'PRIu64' 151 | fprintf(stream," (samples=%" PRIu64 "K",num_samples/METRIC_FACTOR_1K); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:150:26: error: expected ')' before 'PRIu64' 150 | fprintf(stream," (%5" PRIu64 " calls",num_calls); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:153:33: error: expected ')' before 'PRIu64' 153 | fprintf(stream," (samples=%" PRIu64 "",num_samples); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp: In function 'void wflambda::mm_allocator_print_request(FILE*, wflambda::mm_allocator_request_t*, uint64_t, uint64_t)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:421:33: error: expected ')' before 'PRIu64' 421 | fprintf(stream," [#%03" PRIu64 "/%05" PRIu64 "\t%s\t@%08u\t(%" PRIu64 " Bytes)" | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:152:26: error: expected ')' before 'PRIu64' 152 | fprintf(stream," (%5" PRIu64 " call",num_calls); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:167:27: error: expected ')' before 'PRIu64' 167 | fprintf(stream,",%7" PRIu64 " ns/call",ns_per_call); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp: In function 'void wflambda::mm_allocator_print_requests(FILE*, wflambda::mm_allocator_t*, bool)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:457:55: error: expected ')' before 'PRIu64' 457 | fprintf(stream," [n/a\tFree] \t(%" PRIu64 " Bytes)\n",free_block); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:179:28: error: expected ')' before 'PRIu64' 179 | fprintf(stream," {min%" PRIu64 "ns",min_ns); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_timer.cpp:190:27: error: expected ')' before 'PRIu64' 190 | fprintf(stream,",Max%" PRIu64 "ns})\n",max_ns); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp: In function 'void wflambda::mm_allocator_print(FILE*, wflambda::mm_allocator_t*, bool)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:480:45: error: expected ')' before 'PRIu64' 480 | fprintf(stream," => Segments.allocated %" PRIu64 "\n",num_segments); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:481:42: error: expected ')' before 'PRIu64' 481 | fprintf(stream," => Segments.size %" PRIu64 " MB\n",segment_size/(1024*1024)); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:482:45: error: expected ')' before 'PRIu64' 482 | fprintf(stream," => Memory.available %" PRIu64 " MB\n",num_segments*(segment_size/(1024*1024))); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:486:38: error: expected ')' before 'PRIu64' 486 | fprintf(stream," => Memory.used %" PRIu64 "\n",bytes_used); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:487:38: error: expected ')' before 'PRIu64' 487 | fprintf(stream," => Memory.free %" PRIu64 "\n",bytes_free_available+bytes_free_fragmented); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:488:51: error: expected ')' before 'PRIu64' 488 | fprintf(stream," => Memory.free.available %" PRIu64 "\n",bytes_free_available); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/mm_allocator.cpp:489:51: error: expected ')' before 'PRIu64' 489 | fprintf(stream," => Memory.free.fragmented %" PRIu64 "\n",bytes_free_fragmented); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp: In function 'void wflambda::percentage_print(FILE*, const wflambda::profiler_counter_t*, const char*)': /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:274:33: error: expected ')' before 'PRIu64' 274 | fprintf(stream," (samples=%" PRIu64 "G",num_samples/METRIC_FACTOR_1G); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:276:33: error: expected ')' before 'PRIu64' 276 | fprintf(stream," (samples=%" PRIu64 "M",num_samples/METRIC_FACTOR_1M); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:278:33: error: expected ')' before 'PRIu64' 278 | fprintf(stream," (samples=%" PRIu64 "K",num_samples/METRIC_FACTOR_1K); | ~ ^~~~~~~ | ) /isilon/saskatoon-rdc/users/fuf/comDIR/edyeet/src/common/wflign/deps/wflambda/system/profiler_counter.cpp:280:33: error: expected ')' before 'PRIu64' 280 | fprintf(stream," (samples=%" PRIu64 "",num_samples); | ~ ^~~~~~~ | ) gmake[2]: *** [src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/system/profiler_timer.cpp.o] Error 1 gmake[2]: *** Waiting for unfinished jobs.... gmake[2]: *** [src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/system/mm_allocator.cpp.o] Error 1 gmake[2]: *** [src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/system/profiler_counter.cpp.o] Error 1 gmake[1]: *** [src/common/wflign/deps/wflambda/CMakeFiles/wflambda.dir/all] Error 2 gmake[1]: *** Waiting for unfinished jobs.... [ 29%] Linking CXX static library ../../../../../lib/libedlib.a [ 29%] Built target edlib gmake: *** [all] Error 2

cmonat commented 3 years ago

Hello,

I have similar problem when I try to install edyeet. I have the following error messages:

s1060627@usrelhpc02:[~/edyeet-0.3]> module load cmake/3.20.0
s1060627@usrelhpc02:[~/edyeet-0.3]> cmake -H. -Bbuild && cmake --build build -- -j 16
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Setting warning flags
-- Performing Test WOLD_STYLE_CAST
-- Performing Test WOLD_STYLE_CAST - Success
-- Performing Test WSHADOW
-- Performing Test WSHADOW - Success
-- Configuring done
CMake Error in CMakeLists.txt:
  Target "edyeet" requires the language dialect "CXX17" , but CMake does not
  know the compile flags to use to enable it.

CMake Error in src/common/wflign/CMakeLists.txt:
  Target "libwflign_static" requires the language dialect "CXX17" , but CMake
  does not know the compile flags to use to enable it.

CMake Error in src/common/wflign/CMakeLists.txt:
  Target "wflign" requires the language dialect "CXX17" , but CMake does not
  know the compile flags to use to enable it.

CMake Warning (dev) at src/common/wflign/deps/edlib/CMakeLists.txt:54 (add_library):
  Policy CMP0063 is not set: Honor visibility properties for all target
  types.  Run "cmake --help-policy CMP0063" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  Target "edlib" of type "STATIC_LIBRARY" has the following visibility
  properties set for CXX:

    CXX_VISIBILITY_PRESET
    VISIBILITY_INLINES_HIDDEN

  For compatibility CMake is not honoring them for this target.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.

I have tried to set the policy to NEW as suggested but I got this:

s1060627@usrelhpc02:[~/edyeet-0.3]> cmake_policy(SET CMP0063 NEW)
-bash: syntax error near unexpected token `SET'

Do you have an idea how to solve this issue? Thank you very much in advance

Have a great day Cheers C.

subwaystation commented 3 years ago

Hi @cmonat Is your CMake version up to date? https://stackoverflow.com/questions/47238577/target-requires-the-language-dialect-cxx17-with-compiler-extensions-but-cma states that an older CMake version than 3.8 is not compatible with CXX17.

Best, Simon

cmonat commented 3 years ago

Hi @subwaystation I'm using the CMake version 3.20.0 so it should be compatible with CXX17 right ?

Thanks C.

subwaystation commented 3 years ago

I am using the same version, so this is not the issue. What gcc and g++ versions do you have?

subwaystation commented 3 years ago

Whoops, it says right there GNU 4.8.5. This is too old. At least GCC 9.3 is required. Better 10.2.

cmonat commented 3 years ago

Ok thanks, I'll try with GCC 10.2.

cmonat commented 3 years ago

Hello,

I have retried with both cmake 3.20 and gcc 10.2 but I still got the following error message and have no idea how to solve it, somebody have an idea? 

s1060627@usrelhpc02:[~/edyeet-0.3]> cmake -H. -Bbuild && cmake --build build -- -j 16
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Setting warning flags
-- Performing Test WOLD_STYLE_CAST
-- Performing Test WOLD_STYLE_CAST - Success
-- Performing Test WSHADOW
-- Performing Test WSHADOW - Success
-- Configuring done
CMake Error in CMakeLists.txt:
  Target "edyeet" requires the language dialect "CXX17" , but CMake does not
  know the compile flags to use to enable it.

CMake Error in src/common/wflign/CMakeLists.txt:
  Target "libwflign_static" requires the language dialect "CXX17" , but CMake
  does not know the compile flags to use to enable it.

CMake Error in src/common/wflign/CMakeLists.txt:
  Target "wflign" requires the language dialect "CXX17" , but CMake does not
  know the compile flags to use to enable it.

CMake Warning (dev) at src/common/wflign/deps/edlib/CMakeLists.txt:54 (add_library):
  Policy CMP0063 is not set: Honor visibility properties for all target
  types.  Run "cmake --help-policy CMP0063" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  Target "edlib" of type "STATIC_LIBRARY" has the following visibility
  properties set for CXX:

    CXX_VISIBILITY_PRESET
    VISIBILITY_INLINES_HIDDEN

  For compatibility CMake is not honoring them for this target.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.

Thanks in advance Have a great day C.

subwaystation commented 3 years ago

Hi @cmonat The output of your error message still says that CMake is working with GNU 4.8.5. Please fix this. Then it should compile. Best, Simon

cmonat commented 3 years ago

Hi again,

sorry for the delay, I ask for help to the IT service and I did the following to make it work for me:

s1060627@usrelhpc02:[~]> cd edyeet-0.3/
s1060627@usrelhpc02:[~/edyeet-0.3]> ls
bin  build  CMakeCache.txt  CMakeFiles  cmake_install.cmake  CMakeLists.txt  lib  LICENSE  Makefile  README.md  scripts  src
s1060627@usrelhpc02:[~/edyeet-0.3]> rm -rf build/
s1060627@usrelhpc02:[~/edyeet-0.3]> ls
bin  CMakeCache.txt  CMakeFiles  cmake_install.cmake  CMakeLists.txt  lib  LICENSE  Makefile  README.md  scripts  src
s1060627@usrelhpc02:[~/edyeet-0.3]> module load cmake/3.20.0
s1060627@usrelhpc02:[~/edyeet-0.3]> module load gcc/10.2.0
s1060627@usrelhpc02:[~/edyeet-0.3]> export CC=`which gcc`
s1060627@usrelhpc02:[~/edyeet-0.3]> export CXX=`which g++`
s1060627@usrelhpc02:[~/edyeet-0.3]> cmake -H. -Bbuild && cmake --build build -- -j 16

Thanks for your help Have a great day Best, C.

subwaystation commented 3 years ago

Happy to hear that. Thanks for sharing your solution!