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anuradhawick / seq2vec

Fast sequence vectorization for metagenomics analysis. Converts input sequences into oligonucleotide frequency vectors, fast!
MIT License
14 stars 0 forks source link

Installation issue #6

Closed franciscozorrilla closed 6 months ago

franciscozorrilla commented 6 months ago

Hi, I am trying to install seq2vec for oblr but get the following error after running bash build.sh. Not sure if it has to do with some versioning issues, any idea how to fix this?

...updated 16422 targets...
Running CMAKE
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:801 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:19 (find_package)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:801 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:19 (find_package)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:801 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:19 (find_package)

-- Boost version: 1.79.0
-- Found the following Boost libraries:
--   program_options
--   iostreams
-- Configuring done
CMake Error at CMakeLists.txt:21 (add_executable):
  CXX_STANDARD is set to invalid value '20'

-- Generating done

Thanks and best wishes, Francisco

anuradhawick commented 6 months ago

Hi,

Can I know what operating system you're using?

Does your path to the cloned directory contain any spaces?

Also can I see the full bash command output? May be fresh output after cleaning the build directory.

Thanks

franciscozorrilla commented 6 months ago

Thanks for the quick response, for now I will try metacoag as you suggested.

os: Ubuntu 18.04.5 LTS (GNU/Linux 5.4.0-150-generic x86_64) No spaces in filepaths. Full output minus massive list of tagets:

$ bash build.sh 
Downloading boost
boost_1_79_0.tar.gz                                      100%[==================================================================================================================================>] 127.90M   999KB/s    in 83s     
Building boost
Building B2 engine..

###
###
### Using 'gcc' toolset.
###
###

g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

###
###

> g++ -x c++ -std=c++11 -O2 -s -DNDEBUG builtins.cpp class.cpp command.cpp compile.cpp constants.cpp cwd.cpp debug.cpp debugger.cpp execcmd.cpp execnt.cpp execunix.cpp filesys.cpp filent.cpp fileunix.cpp frames.cpp function.cpp glob.cpp hash.cpp hcache.cpp hdrmacro.cpp headers.cpp jam_strings.cpp jam.cpp jamgram.cpp lists.cpp make.cpp make1.cpp md5.cpp mem.cpp modules.cpp native.cpp object.cpp option.cpp output.cpp parse.cpp pathnt.cpp pathsys.cpp pathunix.cpp regexp.cpp rules.cpp scan.cpp search.cpp startup.cpp subst.cpp sysinfo.cpp timestamp.cpp variable.cpp w32_getreg.cpp modules/order.cpp modules/path.cpp modules/property-set.cpp modules/regex.cpp modules/sequence.cpp modules/set.cpp -o b2
> cp b2 bjam
tools/build/src/engine/b2
Detecting Python version... 2.7
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... /usr
Generating B2 configuration in project-config.jam for gcc...

Bootstrapping is done. To build, run:

    ./b2

To generate header files, run:

    ./b2 headers

The configuration generated uses gcc to build by default. If that is
unintended either use the --with-toolset option or adjust configuration, by
editing 'project-config.jam'.

Further information:

   - Command line help:
     ./b2 --help

   - Getting started guide: 
     http://www.boost.org/more/getting_started/unix-variants.html

   - B2 documentation:
     http://www.boost.org/build/

Performing configuration checks

    - default address-model    : 64-bit [1]
    - default architecture     : x86 [1]
    - zlib                     : yes
    - bzip2                    : yes
    - lzma                     : yes
    - zstd                     : no
    - has_lzma_cputhreads builds : yes [2]
    - zlib                     : yes [3]
    - bzip2                    : yes [3]
    - lzma                     : yes [3]
    - zstd                     : no [3]
    - has_lzma_cputhreads builds : no [4]

[1] gcc-7
[2] gcc-7/release/python-2.7/threadapi-pthread/threading-multi/visibility-hidden
[3] link-static
[4] gcc-7/release/link-static/python-2.7/threadapi-pthread/threading-multi/visibility-hidden

Component configuration:

    - atomic                   : not building
    - chrono                   : not building
    - container                : not building
    - context                  : not building
    - contract                 : not building
    - coroutine                : not building
    - date_time                : not building
    - exception                : not building
    - fiber                    : not building
    - filesystem               : not building
    - graph                    : not building
    - graph_parallel           : not building
    - headers                  : not building
    - iostreams                : building
    - json                     : not building
    - locale                   : not building
    - log                      : not building
    - math                     : not building
    - mpi                      : not building
    - nowide                   : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : not building
    - serialization            : not building
    - stacktrace               : not building
    - system                   : not building
    - test                     : not building
    - thread                   : not building
    - timer                    : not building
    - type_erasure             : not building
    - wave                     : not building

...patience...
...found 32465 targets...
...updating 16422 targets...

...

...updated 16422 targets...
Running CMAKE
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:801 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:19 (find_package)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:801 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:19 (find_package)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:801 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:19 (find_package)

-- Boost version: 1.79.0
-- Found the following Boost libraries:
--   program_options
--   iostreams
-- Configuring done
CMake Error at CMakeLists.txt:21 (add_executable):
  CXX_STANDARD is set to invalid value '20'

-- Generating done
-- Build files have been written to: /home/hollfelder/Desktop/HDD/Max/2024_05_06_jungle/oblr/seq2vec/build
anuradhawick commented 6 months ago

@franciscozorrilla this is likely caused by old GCC/CMake versions. Please try to install a later version of cmake and gcc that supports C++ std 20.

Let me know if it resolves.

Following is my latest tool to do kind of the same thing. I am making it so I can guarantee easy install and efficiency

https://github.com/anuradhawick/kmertools

Thanks