Kernel: Bash (Linux)
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].
[0] https://groups.google.com/d/msg/sage-support/a2MS9WALjvo/s1zIfvYpDAAJ
[1] https://github.com/sagemathinc/cocalc/wiki/KubernetesMigration
The failure below has been reported to CoCalc developers. They're on it!
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% 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
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gudhi install-gudhi.ipynb
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/home/user/gudhi/build
The cmake failure below seems related to CGAL:
In [6]:
-- 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]:
In [8]:
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
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# 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)
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