Sharedinstall-gudhi.ipynbOpen in CoCalc
Authors: Corentin Guichaoua, Pierre Guillot, Samuel Lelièvre, Matteo Pennesi, ℏal Snyder
Views : 2

Install GUDHI on CoCalc

Attempting to install GUDHI on CoCalc on 2017-09-12, an error occurs (see below).

Installing GUDHI on CoCalc worked on 2017-08-25, as reported on sage-support [0].

Of course, this was just before the major CoCalc migration [1].

The failure below has been reported to CoCalc developers. They're on it!

In [1]:
URL='https://gforge.inria.fr/frs/download.php/file/37020/' TARBALL='2017-08-22-15-45-31_GUDHI_2.0.1-rc1' TGZ=$TGZ'.tar.gz' DIRNAME='gudhi' curl -C - --retry 99 -o $TGZ $URL$TGZ tar xzf $TGZ mv $TARBALL $DIRNAME
% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 9.9M 100 9.9M 0 0 4884k 0 0:00:02 0:00:02 --:--:-- 4885k
In [2]:
ls
gudhi install-gudhi.ipynb
In [3]:
cd $DIRNAME
In [4]:
mkdir build
In [5]:
cd build/ pwd
/home/user/gudhi/build

The cmake failure below seems related to CGAL:

In [6]:
cmake ..
-- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- 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 -- GUDHI version : 2.0.1-rc1 ++ GUDHI_SUB_DIRECTORIES list is:";test;utilities" ++ GUDHI_MODULES list is:"common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex" -- Found Doxygen: /usr/bin/doxygen (found version "1.8.11") -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.58.0 -- Found the following Boost libraries: -- system -- filesystem -- unit_test_framework -- program_options -- thread -- chrono -- date_time -- atomic -- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so -- GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so -- Found GMPXX: /usr/lib/x86_64-linux-gnu/libgmpxx.so -- GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so CMake Error at /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALExports.cmake:83 (message): The imported target "CGAL::CGAL_Qt5" references the file "/usr/lib/x86_64-linux-gnu/libCGAL_Qt5.so.11.0.1" but this file does not exist. Possible reasons include: * The file was deleted, renamed, or moved to another location. * An install or uninstall procedure did not complete successfully. * The installation package was faulty and contained "/usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALExports.cmake" but not all the files it references. Call Stack (most recent call first): /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALConfig.cmake:12 (include) cmake/modules/GUDHI_third_party_libraries.cmake:26 (find_package) CMakeLists.txt:37 (include) CMake Warning (dev) at /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALExports.cmake:12 (include): Policy CMP0011 is not set: Included scripts do automatic cmake_policy PUSH and POP. Run "cmake --help-policy CMP0011" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The included script /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALExports.cmake affects policy settings. CMake is implying the NO_POLICY_SCOPE option for compatibility, so the effects are applied to the including context. Call Stack (most recent call first): /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALConfig.cmake:12 (include) cmake/modules/GUDHI_third_party_libraries.cmake:26 (find_package) CMakeLists.txt:37 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring incomplete, errors occurred! See also "/home/user/gudhi/build/CMakeFiles/CMakeOutput.log". See also "/home/user/gudhi/build/CMakeFiles/CMakeError.log".
In [7]:
cd /usr/lib/x86_64-linux-gnu/cmake/CGAL/
In [8]:
ls
CGALConfig.cmake FindESBTL.cmake CGALConfig_binary.cmake.in FindEigen3.cmake CGALConfig_install.cmake.in FindF2C.cmake CGALExports-release.cmake FindGLEW.cmake CGALExports.cmake FindGMP.cmake CGAL_CheckCXXFileRuns.cmake FindGMPXX.cmake CGAL_Common.cmake FindIPE.cmake CGAL_CreateSingleSourceCGALProgram.cmake FindLAPACK.cmake CGAL_GeneratorSpecificSettings.cmake FindLEDA.cmake CGAL_Locate_CGAL_TAUCS.cmake FindMKL.cmake CGAL_Macros.cmake FindMPFI.cmake CGAL_SCM.cmake FindMPFR.cmake CGAL_SetupBoost.cmake FindNTL.cmake CGAL_SetupDependencies.cmake FindOpenGL.cmake CGAL_SetupFlags.cmake FindOpenMesh.cmake CGAL_TweakFindBoost.cmake FindQGLViewer.cmake CGAL_UseBLAS.cmake FindQt3-patched.cmake CGAL_UseLAPACK.cmake FindRS.cmake CGAL_UseLEDA.cmake FindRS3.cmake CGAL_UseMKL.cmake FindTAUCS.cmake CGAL_UseMPFI.cmake FindTBB.cmake CGAL_UseRS.cmake Qt3Macros-patched.cmake CGAL_UseRS3.cmake UseCGAL.cmake CGAL_UseTAUCS.cmake UseESBTL.cmake CGAL_VersionUtils.cmake UseEigen3.cmake FindBLAS.cmake UseOpenMesh.cmake FindCGAL.cmake UseTBB.cmake FindCGAL_CORE.cmake test_MPFI.cpp FindCORE.cmake
In [9]:
cat CGALExports.cmake
# Generated by CMake 3.2.2 if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" LESS 2.5) message(FATAL_ERROR "CMake >= 2.6.0 required") endif() cmake_policy(PUSH) cmake_policy(VERSION 2.6) #---------------------------------------------------------------- # Generated CMake target import file. #---------------------------------------------------------------- # Commands may need to know the format version. set(CMAKE_IMPORT_FILE_VERSION 1) # Protect against multiple inclusion, which would fail when already imported targets are added once more. set(_targetsDefined) set(_targetsNotDefined) set(_expectedTargets) foreach(_expectedTarget CGAL::CGAL CGAL::CGAL_ImageIO CGAL::CGAL_Qt5 CGAL::CGAL_Core) list(APPEND _expectedTargets ${_expectedTarget}) if(NOT TARGET ${_expectedTarget}) list(APPEND _targetsNotDefined ${_expectedTarget}) endif() if(TARGET ${_expectedTarget}) list(APPEND _targetsDefined ${_expectedTarget}) endif() endforeach() if("${_targetsDefined}" STREQUAL "${_expectedTargets}") set(CMAKE_IMPORT_FILE_VERSION) cmake_policy(POP) return() endif() if(NOT "${_targetsDefined}" STREQUAL "") message(FATAL_ERROR "Some (but not all) targets in this export set were already defined.\nTargets Defined: ${_targetsDefined}\nTargets not yet defined: ${_targetsNotDefined}\n") endif() unset(_targetsDefined) unset(_targetsNotDefined) unset(_expectedTargets) # Compute the installation prefix relative to this file. get_filename_component(_IMPORT_PREFIX "${CMAKE_CURRENT_LIST_FILE}" PATH) # Use original install prefix when loaded through a # cross-prefix symbolic link such as /lib -> /usr/lib. get_filename_component(_realCurr "${_IMPORT_PREFIX}" REALPATH) get_filename_component(_realOrig "/usr/lib/x86_64-linux-gnu/cmake/CGAL" REALPATH) if(_realCurr STREQUAL _realOrig) set(_IMPORT_PREFIX "/usr/lib/x86_64-linux-gnu/cmake/CGAL") endif() unset(_realOrig) unset(_realCurr) get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH) get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH) get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH) get_filename_component(_IMPORT_PREFIX "${_IMPORT_PREFIX}" PATH) # Create imported target CGAL::CGAL add_library(CGAL::CGAL SHARED IMPORTED) # Create imported target CGAL::CGAL_ImageIO add_library(CGAL::CGAL_ImageIO SHARED IMPORTED) # Create imported target CGAL::CGAL_Qt5 add_library(CGAL::CGAL_Qt5 SHARED IMPORTED) # Create imported target CGAL::CGAL_Core add_library(CGAL::CGAL_Core SHARED IMPORTED) # Load information for each installed configuration. get_filename_component(_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) file(GLOB CONFIG_FILES "${_DIR}/CGALExports-*.cmake") foreach(f ${CONFIG_FILES}) include(${f}) endforeach() # Cleanup temporary variables. set(_IMPORT_PREFIX) # Loop over all imported files and verify that they actually exist foreach(target ${_IMPORT_CHECK_TARGETS} ) foreach(file ${_IMPORT_CHECK_FILES_FOR_${target}} ) if(NOT EXISTS "${file}" ) message(FATAL_ERROR "The imported target \"${target}\" references the file \"${file}\" but this file does not exist. Possible reasons include: * The file was deleted, renamed, or moved to another location. * An install or uninstall procedure did not complete successfully. * The installation package was faulty and contained \"${CMAKE_CURRENT_LIST_FILE}\" but not all the files it references. ") endif() endforeach() unset(_IMPORT_CHECK_FILES_FOR_${target}) endforeach() unset(_IMPORT_CHECK_TARGETS) # This file does not depend on other imported targets which have # been exported from the same project but in a separate export set. # Commands beyond this point should not need to know the version. set(CMAKE_IMPORT_FILE_VERSION) cmake_policy(POP)
In [10]:
which CGAL
In [ ]: