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ekg / seqwish

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MIT License
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I can't install seqwish on any computer #51

Closed Flavia95 closed 4 years ago

Flavia95 commented 4 years ago

Hi, I use this command for install seqwish: 

sudo apt install build-essential cmake zlib1g-dev
cmake -H. -Bbuild && cmake --build build -- -j3

I always get the same error on different computers with Ubuntu.

-- The C compiler identification is GNU 8.4.0
-- The CXX compiler identification is GNU 8.4.0
-- 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
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE  
CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
 No download info given for 'sdsl-lite' and its source directory:
/home/tools/seqwish/0.6/deps/sdsl-lite
is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:29 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
 No download info given for 'tayweeargs' and its source directory:

 /home/tools/seqwish/0.6/deps/args
is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:41 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'gzipreader' and its source directory:

  /home/tools/seqwish/0.6/deps/gzip_reader
 is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:49 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'mmmulti' and its source directory:

   /home/tools/seqwish/0.6/deps/mmmulti
 is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:57 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'iitii' and its source directory:

   /home/tools/seqwish/0.6/deps/iitii

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:67 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'mmap_allocator' and its source directory:

   /home/tools/seqwish/0.6/deps/mmap_allocator

is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:76 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'ips4o' and its source directory:

   /home/tools/seqwish/0.6/deps/ips4o

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:85 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'bbhash' and its source directory:

   /home/tools/seqwish/0.6/deps/BBHash

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:94 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'atomicbitvector' and its source directory:

   /home/tools/seqwish/0.6/deps/atomicbitvector

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:104 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'atomicqueue' and its source directory:

   /home/tools/seqwish/0.6/deps/atomic_queue

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:114 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'ska' and its source directory:
 /home/tools/seqwish/0.6/deps/flat_hash_map
is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:124 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message):
  No download info given for 'paryfor' and its source directory:

   /home/tools/seqwish/0.6/deps/paryfor

  is not an existing non-empty directory.  Please specify one of:

   * SOURCE_DIR with an existing non-empty directory
   * DOWNLOAD_COMMAND
   * URL
   * GIT_REPOSITORY
   * SVN_REPOSITORY
   * HG_REPOSITORY
   * CVS_REPOSITORY and CVS_MODULE
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command)
  CMakeLists.txt:134 (ExternalProject_Add)

-- Configuring incomplete, errors occurred!
See also "/home/tools/seqwish/0.6/build/CMakeFiles/CMakeOutput.log".
See also "/home/tools/seqwish/0.6/build/CMakeFiles/CMakeError.log".
ekg commented 4 years ago

Please use git clone --recursive to obtain the repo. If you already have the repo, then you can use git submodules update --init --recursive.

On Sun, May 3, 2020, 21:41 Flavia Villani notifications@github.com wrote:

Hi, I use this command for install seqwish:

sudo apt install build-essential cmake zlib1g-dev cmake -H. -Bbuild && cmake --build build -- -j3

I always get the same error on different computers with Ubuntu.

-- The C compiler identification is GNU 8.4.0 -- The CXX compiler identification is GNU 8.4.0 -- 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 -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'sdsl-lite' and its source directory: /home/tools/seqwish/0.6/deps/sdsl-lite is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:29 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'tayweeargs' and its source directory:

/home/tools/seqwish/0.6/deps/args is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:41 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'gzipreader' and its source directory:

/home/tools/seqwish/0.6/deps/gzip_reader is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:49 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'mmmulti' and its source directory:

/home/tools/seqwish/0.6/deps/mmmulti is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:57 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'iitii' and its source directory:

/home/tools/seqwish/0.6/deps/iitii

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:67 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'mmap_allocator' and its source directory:

/home/tools/seqwish/0.6/deps/mmap_allocator

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:76 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'ips4o' and its source directory:

/home/tools/seqwish/0.6/deps/ips4o

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:85 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'bbhash' and its source directory:

/home/tools/seqwish/0.6/deps/BBHash

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:94 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'atomicbitvector' and its source directory:

/home/tools/seqwish/0.6/deps/atomicbitvector

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:104 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'atomicqueue' and its source directory:

/home/tools/seqwish/0.6/deps/atomic_queue

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:114 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'ska' and its source directory: /home/tools/seqwish/0.6/deps/flat_hash_map is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:124 (ExternalProject_Add)

CMake Error at /usr/share/cmake-3.10/Modules/ExternalProject.cmake:2474 (message): No download info given for 'paryfor' and its source directory:

/home/tools/seqwish/0.6/deps/paryfor

is not an existing non-empty directory. Please specify one of:

  • SOURCE_DIR with an existing non-empty directory
  • DOWNLOAD_COMMAND
  • URL
  • GIT_REPOSITORY
  • SVN_REPOSITORY
  • HG_REPOSITORY
  • CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.10/Modules/ExternalProject.cmake:3029 (_ep_add_download_command) CMakeLists.txt:134 (ExternalProject_Add)

-- Configuring incomplete, errors occurred! See also "/home/tools/seqwish/0.6/build/CMakeFiles/CMakeOutput.log". See also "/home/tools/seqwish/0.6/build/CMakeFiles/CMakeError.log".

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Flavia95 commented 4 years ago

Thanks, it works well. Please, update the installation guide (like odgi's one).