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Hi,

I'm trying to build Seg3D2 on Ubuntu 17.10.

I download Seg3D-2.2.1.tar.gz from

https://www.sci.utah.edu/releases/seg3d_v2.2.1/Seg3D-2.2.1.tar.gz

and unpack it to ~/Downloads/Seg3D-2.2.1. Running the build script gives the
errors shown at the end of the message.

Doing some digging, I think there are some external dependencies that Seg3d
expects to download of install somewhere, but are not there. For example, the
error below says that Tetgen cannot be found. In file bin/Externals/Source/
ImplicitFunction_external/.travis.yml, there's a section for Tetgen

#before_script:
script:
# build Tetgen dependency
- mkdir build
- cd build
- tar xzf $HOME/deps/tetgen1.4.3.tar.gz
- pushd tetgen1.4.3
- make tetlib
- tar xzf $HOME/deps/tetgen_cmake.tgz
- popd


so I think file tetgen1.4.3.tar.gz needs to go somewhere in the Seg3D2 tree.
I've tried putting it in bin/Externals/Source/ImplicitFunction_external, and
also in ~/deps, but the build keeps failing with the same error.


<ERROR>
$ ./build.sh
Build platform is Linux.
Parsing arguments...
CMake args:
Make Flags:
Build Type: Release
/usr/bin/cmake version 3.9.1 found
cmakebin=/usr/bin/cmake
cd /home/rcasero/Downloads/Seg3D-2.2.1/bin
/usr/bin/cmake /home/rcasero/Downloads/Seg3D-2.2.1/Superbuild -
DBUILD_DOCUMENTATION:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release -
DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
-- The C compiler identification is GNU 7.2.0
-- The CXX compiler identification is GNU 7.2.0
-- 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
-- Found Git: /usr/bin/git (found version "2.14.1")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found suitable version "4.8.7", minimum required
is "4.6.0")
-- QTVERSION=4.8.7
-- Found use file: /usr/share/cmake-3.9/Modules/UseQt4.cmake
-- Zlib_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
Zlib_external
-- Glew_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
Glew_external
-- Freetype_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
Freetype_external
-- SQLite_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
SQLite_external
-- LibPNG_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
LibPNG_external
-- Python_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Install/
Python_external
-- ITK_DIR=/home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
ITK_external
CMake Warning (dev) at /usr/share/cmake-3.9/Modules/ExternalProject.cmake:1183
(if):
Policy CMP0054 is not set: Only interpret if() arguments as variables or
keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

Quoted variables like "regex" will no longer be dereferenced when the
policy is set to NEW. Since the policy is not set the OLD behavior will be
used.
Call Stack (most recent call first):
/usr/share/cmake-3.9/Modules/ExternalProject.cmake:2241
(_ep_command_line_to_initial_cache)
/usr/share/cmake-3.9/Modules/ExternalProject.cmake:2305
(_ep_extract_configure_command)
/usr/share/cmake-3.9/Modules/ExternalProject.cmake:2568
(_ep_add_configure_command)
BoostExternal.cmake:76 (ExternalProject_Add)
Superbuild.cmake:203 (INCLUDE)
CMakeLists.txt:33 (INCLUDE)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Boost_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Install/
Boost_external
-- Teem_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
Teem_external
-- ImplicitFunction_DIR: /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/
Build/ImplicitFunction_external
-- Configuring done
-- Generating done
-- Build files have been written to: /home/rcasero/Downloads/Seg3D-2.2.1/bin
Building SCIRun using make...
make
Scanning dependencies of target Data_external
[ 1%] Creating directories for 'Data_external'
[ 2%] Performing download step (git clone) for 'Data_external'
Cloning into 'Seg3DData'...
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

git checkout -b <new-branch-name>

HEAD is now at 6470e08... Tooth is a nice simple test dataset.
[ 3%] No patch step for 'Data_external'
[ 4%] Performing update step for 'Data_external'
Current branch HEAD is up to date.
[ 5%] No configure step for 'Data_external'
[ 6%] No build step for 'Data_external'
[ 7%] No install step for 'Data_external'
[ 8%] Completed 'Data_external'
[ 8%] Built target Data_external
Scanning dependencies of target ImplicitFunction_external
[ 9%] Creating directories for 'ImplicitFunction_external'
[ 10%] Performing download step (git clone) for 'ImplicitFunction_external'
Cloning into 'ImplicitFunction_external'...
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

git checkout -b <new-branch-name>

HEAD is now at a59711d... Disable NRRD IO for now.
[ 11%] No patch step for 'ImplicitFunction_external'
[ 12%] Performing update step for 'ImplicitFunction_external'
Current branch HEAD is up to date.
[ 13%] Performing configure step for 'ImplicitFunction_external'
loading initial cache file /home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/
tmp/ImplicitFunction_external/ImplicitFunction_external-cache-Release.cmake
-- The C compiler identification is GNU 7.2.0
-- The CXX compiler identification is GNU 7.2.0
-- 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
-- Found GTest: /usr/local/lib/libgtest.a (Required is at least version "1.7")
-- 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
-- Could NOT find Tetgen (missing: Tetgen_DIR)
CMake Error at CMakeLists.txt:62 (message):
Tetgen library not found in Tetgen_DIR-NOTFOUND


-- Configuring incomplete, errors occurred!
See also "/home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
ImplicitFunction_external/CMakeFiles/CMakeOutput.log".
See also "/home/rcasero/Downloads/Seg3D-2.2.1/bin/Externals/Build/
ImplicitFunction_external/CMakeFiles/CMakeError.log".
CMakeFiles/ImplicitFunction_external.dir/build.make:105: recipe for target
'Externals/Stamp/ImplicitFunction_external/ImplicitFunction_external-
configure' failed
make[2]: *** [Externals/Stamp/ImplicitFunction_external/
ImplicitFunction_external-configure] Error 1
CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/
ImplicitFunction_external.dir/all' failed
make[1]: *** [CMakeFiles/ImplicitFunction_external.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
Building Seg3D returned an error

Either the code failed to build properly or

the testing programs failed to complete without

every single test program passing the test.
</ERROR>

Best regards,

Ramon.

---

• [Seg3D] Build on Ubuntu 17.10 Artful fails, rcasero, 04/10/2018
  • Re: [Seg3D] Build on Ubuntu 17.10 Artful fails, rcasero, 04/12/2018
    • Re: [Seg3D] Build on Ubuntu 17.10 Artful fails, Mark Dewey, 04/12/2018

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