Documentation/4.10/Developers/Build Instructions

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For the latest Slicer documentation, visit the read-the-docs.


Contents

PREREQUISITES

For all systems be sure git-lfs is properly installed for use with VTKv9 (required for VTKm checkout)

As of early 2018, Slicer migrated to Qt5. See instructions at this labs page for the new requirements: https://www.slicer.org/wiki/Documentation/Labs/Qt5-and-VTK8


The prerequisites listed below are required to be able to configure/build/package/test Slicer.

Linux

  • CMake >= 3.7-rc02
  • Git >= 1.7.10
  • Svn >= 1.7
  • Qt 5.11: tested and recommended
    • To build Slicer: install Qt using the distribution package manager.
    • To package and redistribute Slicer: download and execute qt-unified-linux-x64-online.run, install Qt, make sure to select qtscript and qtwebengine components.
  • Qt 4.8.7. See details here. See some history here (Note that any version >= Qt 4.7.4 can be used only for Ubuntu < 12.04)
  • GCC suite

Debian

  • Debian squeeze/wheezy/testing(jessie) users, start by pasting the following lines in a terminal
sudo apt-get install subversion git-core git-svn
sudo apt-get install build-essential libx11-dev libxt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev libfontconfig-dev libxrender-dev libncurses5-dev
sudo apt-get install cmake
sudo apt-get install qt-sdk


Ubuntu

Common Prerequisites
sudo apt-get install subversion git-core git-svn

sudo apt-get install make gcc g++ libx11-dev libxt-dev libgl1-mesa-dev libglu1-mesa-dev libfontconfig-dev libxrender-dev libncurses5-dev

sudo apt-get install libosmesa6-dev  # Only for Ubuntu < 14.04.3
  1. On Ubuntu 14.04.3 LTS, attempting to install libosmesa6-dev results in an error.
    The following packages have unmet dependencies:
 libosmesa6-dev : Depends: libosmesa6 (= 10.1.3-0ubuntu0.4) but it is not going to be installed
 E: Unable to correct problems, you have held broken packages.

    For more details, see Bug 1424059.

  1. Slicer compiles successfully without that package, but VTK_OPENGL_HAS_OSMESA is disabled.
  • For Qt5.5 on Ubuntu 16.04
sudo apt-get install libgstreamer-plugins-base0.10-dev
CMake
  1. Open a terminal and copy the command reported below
  2. Download stable version of CMake and extract the archive: 
    sudo apt-get install curl
mkdir ~/Support && cd ~/Support
curl -O https://cmake.org/files/v3.8/cmake-3.8.2-Linux-x86_64.tar.gz
tar -xzvf cmake-3.8.2-Linux-x86_64.tar.gz
  3. Create symbolic links into ~/bin 
    mkdir -p ~/bin
for name in cmake ctest cpack ccmake cmake-gui; do
  ln -s ~/Support/cmake-3.8.2-Linux-x86_64/bin/$name ~/bin/$name
done
  1. You MUST download the standard CMake binary because the distributed version of CMake cannot be used to build slicer.
    See here for more details.
Qt 4 (deprecated)

Ubuntu 14.04 and above: Qt 4 == 4.8.7 MUST be used.

See https://github.com/jcfr/qt-easy-build

or on ubuntu 16.04 and 16.10, you can also install qt4.8.7 with: 

sudo apt-get install qt4-dev-tools libqt4-dev libqt4-core libqt4-gui libqtwebkit-dev

or if that fails (due to libqt4-core and libqt4-gui packages not found): 

sudo apt-get install qt4-dev-tools libqt4-dev libqtcore4 libqtgui4 libqtwebkit-dev

Ubuntu 12.04, 12.10, 13.04 and 13.10: Qt 4 >= 4.8.5 MUST be used. 

cd ~/Support   # This is where we will build Qt and dependent libraries
 
# Keep track of our working directory
cwd=$(pwd)

# This will download, then build zlib and openssl in the current folder
rm -f get-and-build-openssl-for-slicer.sh
wget https://gist.githubusercontent.com/jcfr/9513568/raw/004d4af8829c95690da2af51eaa3f0c64b7c4e02/get-and-build-openssl-for-slicer.sh
chmod u+x get-and-build-openssl-for-slicer.sh 
./get-and-build-openssl-for-slicer.sh 

# This will download Qt source in the current folder
wget http://packages.kitware.com/download/item/6175/qt-everywhere-opensource-src-4.8.6.tar.gz
echo "2edbe4d6c2eff33ef91732602f3518eb  qt-everywhere-opensource-src-4.8.6.tar.gz" > qt-everywhere-opensource-src-4.8.6.tar.gz.md5
md5sum -c qt-everywhere-opensource-src-4.8.6.tar.gz.md5

# This will configure and build Qt in RELEASE against the zlib and openssl previously built
tar -xzvf qt-everywhere-opensource-src-4.8.6.tar.gz
mv qt-everywhere-opensource-src-4.8.6 qt-everywhere-opensource-release-src-4.8.6
mkdir qt-everywhere-opensource-release-build-4.8.6
cd qt-everywhere-opensource-release-src-4.8.6
./configure -prefix $cwd/qt-everywhere-opensource-release-build-4.8.6    \
                   -release \
                   -opensource -confirm-license \
                   -no-qt3support \
                   -webkit \
                   -nomake examples -nomake demos \
                   -openssl -I $cwd/openssl-1.0.1e/include   -L $cwd/openssl-1.0.1e \
&& make -j7 && make install

For more details, consider reading the FAQ entry: Why Qt 4 >= 4.8.5 should be used on Ubuntu 12.04 and above ?

CentOS

See instructions reported in qt5-centos7/Dockerfile


MacOSX

  • XCode command line tools must be installed:
 xcode-select --install
  • El Capitan is what most developers use.
  • CMake 3.7-rc02 is recommended. Check the minimum required CMake version here
  • Qt 5: tested and recommended.
    • For building Slicer: download and execute qt-unified-mac-x64-online.dmg, install Qt 5.10, make sure to select qtscript and qtwebengine components.
    • For packaging and redistributing Slicer: build Qt using qt-easy-build

MacOSX 10.9.4 (Mavericks)

(1) Make sure to install this update: http://support.apple.com/kb/DL1754

(2) Use CMake 3.0.1 - it is known to be working and is supported (if you want to use CMake already installed on your system, 2.8.12.2 is known to work on Mac OS X 10.9.5) 

$ curl -O http://www.cmake.org/files/v2.8/cmake-2.8.11-Darwin64-universal.tar.gz
$ tar -xzvf cmake-2.8.11-Darwin64-universal.tar.gz --strip-components=1

$ CMake\ 2.8-11.app/Contents/bin/cmake --version
cmake version 2.8.11
  • Git >= 1.7.10
  • Svn >= 1.7
  • XCode (for the SDK libs)
    • After installing XCode, install XCode command line developer tools:
xcode-select --install

Mac OSX 10.11 (El Capitan)

XCode up to version 7 is known to work for Slicer compilation. XCode 8 breaks things on several levels for now. Remember to install XCode command line tools (see above) if a reinstall for XCode is needed.

The standard Qt4 installers fail on this version and the 4.8.6 source code won't build. But as described on the slicer-devel mailing list it is possible to install the homebrew version of qt4 which patches it to work on El Capitan (see below).

  • Install the OS, Xcode, and XQuartz (see MacOSX 10.10 above)
  • Install Qt4 by running the following two commands:
brew install qt4
xcode-select --install
  • TCL does not build correctly on El Capitan as of 2015-12-03, so when building Slicer turn `Slicer_USE_PYTHONQT_WITH_TCL` off.

Mac OSX 10.12 (Sierra)

Similar to 10.11 (El Capitan), there are new issues with Qt4 (caused by Phonon). The GitHub user Cartr offered a patch to the brew team, and even though it was not integrated (the homebrew team decided to stop patching their recipe to encourage people to use Qt5), he turned his formula into a tap that can be installed (see below).

Follow instructions for 10.11 (Installing Xcode, XQuartz, run without TCL) but install Qt4 like shown below instead: 

brew install cartr/qt4/qt
xcode-select --install

Confirmed with Xcode:

  • Version 8.1 (8B62) and cmake version 3.4.20151021-g8fbc8e
  • Version 8.3.3 and cmake 3.5.2

Windows

Common Prerequisites

  • CMake >= 3.0 (3.7.1 recommended)
  • Git >= 1.7.10
    • Note For convenience, you could update the PATH variable so that git can be automatically discovered when configuring Slicer. If not, you will have to specify the GIT_EXECUTABLE at configure time.
  • Subversion (SVN) client: any SVN client that has command line tools
    • SlikSvn , or
    • TortoiseSVN - make sure you install Command line client tools component (disabled by default)
  • NSIS (optional): Needed if packaging Slicer - Click here to download. Make sure you install the language packs.
  • Qt:
    • Qt5 recommended and officially supported. Download qt-unified-windows-x86-online.exe and install Qt along with qtscript and qtwebengine components. For building with VS2015, Qt version 5.10.x or older is required. For more details, read step-by-step guide.
    • Qt 4: will still work until Slicer-4.10 but not officially supported. See details here.

Tested and recommended build environment

Experimental/deprecated build environments

  • Visual Studio 2017 (Community or any other edition) with VS2015 build tools (tested, works well)
    • When configuring Visual Studio installer, enable installation of component VC++ 2015.3 v14.00 (v140) toolset for desktop
    • Visual Studio 2015 toolset must be set in CMake: Optional toolset to use (argument to -T) need to be set to v140
  • Visual Studio 2013 with Update 5 (deprecated, should still work)
    • As of commit 7160260: Slicer compilation is successful, with some caveats.
    • Build Qt 4.8.7 with SSL support using qt-easy-build.
    • Note: be sure to pick the version of qmake that you built in the earlier steps if applicable (CMake may pick a different qmake, for example if installed with anaconda)
  • VS2012 (untested, may work)
  • VS2010 (untested, probably does not work)
    • Microsoft Visual Studio 2010 (Any edition)
    • Make sure to build or install:
      • Qt 4.8
    • Make sure to install:
      • SP1. Click here to download SP1 and click here to understand the motivation.
      • SP1 Compiler update. Click here to download and here to understand the motivation.
  • VS2008 (untested, probably does not work)
  • Cygwin (untested, probably does not work)
    • Cygwin suite (building with cygwin gcc not supported, but the cygwin shell environment can be used to run git, svn, etc).






CHECKOUT slicer source files


Check out the code using git and configure the git svn bridge:

  1. While it is not enforced, we strongly recommend you to AVOID the use of SPACES for both the source directory and the build directory. We mean it.
  1. Due to maximum path length limitations during build the build process, source and build folders must be located in a folder with very short total path length. This is expecially critical on Windows. For example, C:\D\S4 for source and C:\D\S4R for release-mode build folder works.

  1. Clone the github repository

    cd MyProjects
git clone git://github.com/Slicer/Slicer.git

    The Slicer directory is automatically created after cloning Slicer.

  2. Setup the development environment:

    cd Slicer
./Utilities/SetupForDevelopment.sh

    For more details see Development With Git.

    On Windows enter the commands above in to a bash shell, such as Git Bash (part of msysgit) or use a Git client with a graphical user interface.

  3. Configure the git svn bridge to ensure the mapping with svn revision.

    git-svn is only required for core developers with svn access - other people can skip it.

    cd Slicer
git svn init http://svn.slicer.org/Slicer4/trunk
git update-ref refs/remotes/git-svn refs/remotes/origin/master
git checkout master
git svn rebase
    4. Note for Mac OSX El Capitan:

    You might need to link SVN from XCode if you find that git svn is broken. To get correct links and bypass El Capitan's SIP use these commands 

    sudo mkdir /Library/Perl/5.18/auto
sudo ln -s /Applications/Xcode.app/Contents/Developer/Library/Perl/5.18/darwin-thread-multi-2level/SVN /Library/Perl/5.18/darwin-thread-multi-2level
sudo ln -s /Applications/Xcode.app/Contents/Developer/Library/Perl/5.18/darwin-thread-multi-2level/auto/SVN /Library/Perl/5.18/auto/

    If you plan to compile Slicer to develop your own extensions and test these extensions on Slicer releases, it is convenient to download the source code directly from SVN and specify the revision number corresponding to the release you want. To do so, replace <MARKER> and <SVNREVISION> in the command below with the selected revision and marker: 

    svn co http://svn.slicer.org/Slicer4/<MARKER> Slicer-r<SVNREVISION> -r <SVNREVISION>

     Release             SVN revision#       Marker
 4.8.1               26813               branches/Slicer-4-8
 4.8.0               26489               trunk
 4.6.2               25516               branches/Slicer-4-6
 4.5.0-1             24735               trunk
 4.4                 23774               trunk
 4.3.1               22599               branches/Slicer-4-3
 4.3.0               22408               trunk

    More corresponding SVN revision numbers can be found here and here. The <MARKER> can be found at the bottom of this page http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=SVNREVISION by replacing SVNREVISION with the selected revision.

    For example, to checkout the source code associated with revision 4.8.1, you would use the following command: 

    svn co http://svn.slicer.org/Slicer4/branches/Slicer-4-8 Slicer-r26813 -r 26813







CONFIGURE and generate Slicer solution files

There are many ways of customizing Slicer's user interface or feature set. This section describes how a custom Slicer build can be configured at build-time. See an overview of various other options in this presentation.

You can configure and generate Slicer solution files using either ccmake or cmake-gui.

Customizing application build

Customized editions of Slicer can be generated without changing Slicer source code, just by modifying CMake variables:

  • SlicerApp_APPLICATION_NAME: Custom application name to be used, instead of default "Slicer". The name is used in installation package name, window title bar, etc.
  • Slicer_DISCLAIMER_AT_STARTUP: String that is displayed to the user after first startup of Slicer after installation (disclaimer, welcome message, etc).
  • Slicer_DEFAULT_HOME_MODULE: Module name that is activated automatically on application start.
  • Slicer_DEFAULT_FAVORITE_MODULES: Modules that will be added to the toolbar by default for easy access. List contains module names, separated by space character.
  • Slicer_CLIMODULES_DISABLED: Built-in CLI modules that will be removed from the application. List contains module names, separated by semicolon character.
  • Slicer_QTLOADABLEMODULES_DISABLED: Built-in Qt loadable modules that will be removed from the application. List contains module names, separated by semicolon character.
  • Slicer_QTSCRIPTEDMODULES_DISABLED: Built-in scripted loadable modules that will be removed from the application. List contains module names, separated by semicolon character.
  • Slicer_USE_PYTHONQT_WITH_OPENSSL: enable/disable building the application with SSL support (ON/OFF)
  • Slicer_USE_SimpleITK: enable/disable SimpleITK support (ON/OFF)
  • Slicer_BUILD_SimpleFilters: enable/disable building SimpleFilters. Requires SimpleITK. (ON/OFF)
  • Slicer_BUILD_EMSegment: enable/disable building EM segmenter (ON/OFF)
  • Slicer_USE_PYTHONQT_WITH_TCL: TCL support (ON/OFF)
  • Slicer_EXTENSION_SOURCE_DIRS: Defines additional extensions that will be included in the application package as built-in modules. Full paths of extension source directories has to be specified, separated by semicolons.

Per-platform instructions

Windows

Recommended: run CMake (cmake-gui) from the Windows Start menu

  • Set the build directory. For example: C:\Slicer-SuperBuild-Debug or C:\Slicer-SuperBuild-Release.
    • Because Windows doesn't support file path longer than 260 characters and has a maximum command line length, please make sure that the total path name of your Slicer-build directory is no longer than 50 characters (for example c:\work\Slicer\Slicer-SuperBuild may work). In case of any build error, use very short directory names: C:\S4 for source directory, C:\S4D for debug build, C:\S4R for release build.
    • You cannot use the same build tree for both release or debug mode builds. If both build types are needed, then the same source directory can be used, but a separate build directory should be created and configured for each build type.
  • Select your compiler: Visual Studio 14 2015 Win64
  • Do not configure yet.
  • Add Qt5_DIR variable pointing to Qt5 folder such as C:\Qt\5.10.0\msvc2015_64\lib\cmake\Qt5.
  • Configure
  • Click generate then close cmake-gui.
  • If building in release mode:
    • Open the top-level Slicer.sln file in the build directory in Visual Studio
    • Set active configuration to Release. Visual Studio will select Debug build configuration by default when you first open the solution in the Visual Studio GUI. If you build Slicer in release mode and accidentally forget to switch the build configuration to Release then the build will fail. Note: you can avoid this manual configuration mode selection by setting CMAKE_CONFIGURATION_TYPES to Release in cmake-gui.
  • If building in debug mode:
  • Build the ALL_BUILD project

Alternative option: Configure and build using command-line or batch file

Instead of using CMake (cmake-gui), it is also possible to configure by creating a .bat file that contains command-line instructions and run this .bat file each time a Slicer needs to be re-built. The examples below assume Slicer source code is in C:\S4 folder and Qt-5.10 is installed in default location.

Visual Studio 2015 in Release mode: 

mkdir C:\D\S4R
cd /d C:\D\S4R
"C:\Program Files\CMake\bin\cmake.exe" -G "Visual Studio 14 2015 Win64" -DQt5_DIR:PATH=C:\Qt\5.10.0\msvc2015_64\lib\cmake\Qt5 C:\D\S4
"C:\Program Files\CMake\bin\cmake.exe" --build . --config Release

Visual Studio 2015 in Debug mode: 

mkdir C:\D\S4D
cd /d C:\D\S4D
"C:\Program Files\CMake\bin\cmake.exe" -G "Visual Studio 14 2015 Win64" -DQt5_DIR:PATH=C:\Qt\5.10.0\msvc2015_64\lib\cmake\Qt5 C:\D\S4
"C:\Program Files\CMake\bin\cmake.exe" --build . --config Debug

Visual Studio 2017 with VS2015 toolset in Release mode: 

mkdir C:\D\S4R
cd /d C:\D\S4R
"C:\Program Files\CMake\bin\cmake.exe" -G "Visual Studio 15 2017 Win64" -DQt5_DIR:PATH=C:\Qt\5.10.0\msvc2015_64\lib\cmake\Qt5 C:\D\S4
"C:\Program Files\CMake\bin\cmake.exe" --build . --config Release

Unix-like

  • Recommended:
    • Configure using the following commands. By default CMAKE_BUILD_TYPE is set to Debug.
mkdir Slicer-SuperBuild-Debug
cd Slicer-SuperBuild-Debug
cmake -DCMAKE_BUILD_TYPE:STRING=Debug -DQt5_DIR:PATH=/path/to/Qt5.11.0/5.11.0/gcc_64/lib/cmake/Qt5 ../Slicer

where you replace /path/to/QtSDK with the real path on your machine where QtSDK is located

If using Qt from the system, do not forget to add the following CMake variable to your configuration command line: 

-DSlicer_USE_SYSTEM_QT:BOOL=1
  • Remarks:
  1. Instead of cmake, you can use ccmake or cmake-gui to visually inspect and edit configure options.
  2. Using top-level directory name like Slicer-SuperBuild-Release or Slicer-SuperBuild-Debug is recommended.
  3. Step-by-step debug instuctions
  • On Mac OS X 10.9 (Mavericks) / 10.10 (Yosemite) / 10.11 (El Capitan), also set the following variables (see discussion):
Variable Description
Slicer_USE_PYTHONQT_WITH_TCL OFF
CMAKE_OSX_DEPLOYMENT_TARGET 10.9 or 10.10 or 10.11

General information

Two projects are generated by either cmake, ccmake or cmake-gui.

One of them is in the top-level bin directory Slicer-SuperBuild and the other one is in the subdirectory Slicer-build: 

Slicer-SuperBuild/Slicer-build
  1. The first project in Slicer-SuperBuild manages all the external dependencies of Slicer (VTK, ITK, Python, ...). To build Slicer for the first time, run make (or build the solution file in Visual Studio) in Slicer-SuperBuild, which will update and build the external libraries and if successful will then build the subproject Slicer-build.
  2. The second project in Slicer-SuperBuild/Slicer-build is the "traditional" build directory of Slicer. After local changes in Slicer (or after an svn update on the source directory of Slicer), only running make (or building the solution file in Visual Studio) in Slicer-SuperBuild/Slicer-build is necessary (the external libraries are considered built and up to date).
  3. Warning: An significant amount of disk space is required to compile Slicer in Debug (>10GB on Windows)

Workaround for if the firewall is blocking git protocol

  • Some firewalls will block the git protocol. A possible workaround is to configure Slicer by disabling the option Slicer_USE_GIT_PROTOCOL. Then the http protocol will be used instead. Consider also reading https://github.com/commontk/CTK/issues/33






BUILD Slicer

After configuration, start the build process in the Slicer-SuperBuild directory

Linux or MacOSX (Makefile) Windows (Visual Studio)

Start a terminal. 

$ cd ~/Projects/Slicer-SuperBuild

$ make -j<NUMBEROFCORES>

In case of file download hash mismatch error, you need to acquire the latest wget, and build cmake with OpenSSL turned on. For more information, see here and here

Start Windows Explorer. Need help?

  1. Open Slicer-SuperBuild\Slicer.sln in Visual Studio
  2. Select build configuration. Usually Release or Debug
  3. Select menu Project -> Build Solution

If you make local changes to Slicer, open the solution file located in the directory Slicer-SuperBuild/Slicer-build instead. You should then be able to either build all projects or just a specific one.






RUN Slicer

Linux or MacOSX Windows

Start a terminal. 

$ Slicer-SuperBuild/Slicer-build/Slicer

Start Windows Explorer. Need help?

Run Slicer-SuperBuild/Slicer-build/Slicer.exe

Notes:

  • Linux Ubuntu: if you have odd rendering artifacts, try disabling visual effects (System/Appearance/Visual Effects)
  • Windows: If build was OK, but Slicer doesn't start (e.g. gives the error: [bin/Release/SlicerQT-real.exe] exit abnormally - Report the problem.) then one possible root cause is that you have a copy of Python26.dll in your windows system directory (e.g., c:\Windows\System32\python26.dll). The solution is to rename or remove the python dll in the system directory. See more details here: http://www.na-mic.org/Bug/view.php?id=1180






TEST Slicer

After building, run the tests in the Slicer-SuperBuild/Slicer-build directory

Linux or MacOSX (Makefile) Windows (Visual Studio)

Start a terminal. 

$ cd ~/Projects/Slicer-SuperBuild/Slicer-build

$ ctest -j<NUMBEROFCORES>

Start Windows Explorer. Need help?

  1. Open Slicer-SuperBuild\Slicer.sln in Visual Studio
  2. Select build configuration. Usually Release or Debug
  3. In the Solution Explorer, right click on RUN_TESTS project and then select Build

Note: RUN_TESTS project can be found in the CMakePredefinedTargets folder. See here for more details.

Slicer-vs2013-CMakePredefinedTargets-RUN TESTS.png






PACKAGE Slicer

Linux or MacOSX (Makefile) Windows (Visual Studio)

Start a terminal. 

$ cd ~/Projects/Slicer-SuperBuild
$ cd Slicer-build

$ make package

Note: Make sure to patch VS2008 using the script fix-vc9-redist-manifests.ps1
Start Windows Explorer. Need help?

  1. Open Slicer-SuperBuild\Slicer-build\Slicer.sln in Visual Studio
  2. Select Release build configuration.
  3. In the Solution Explorer, right click on PACKAGE project in group CMakePredefinedTargets and then select Build

Note: PACKAGE project can be found in the CMakePredefinedTargets folder. See here for more details.

Slicer-vs2013-CMakePredefinedTargets-PACKAGE.png


Common errors

CMake complains during configuration

CMake may not directly show what's wrong; try to look for log files of the form BUILD/CMakeFiles/*.log (where BUILD is your build directory) to glean further information.

A tool returned an error code from "Generating vtksysProcessFwd9xEnc.c"

The application has failed to start because its side-by-side configuration is incorrect.
Please see the application event log or use the command-line sxstrace.exe tool for more detail.
Project : error PRJ0019: A tool returned an error code from "Generating
vtksysProcessFwd9xEnc.c"

Suggested solution: Install SP1 of Visual Studio

See also:

error: ‘class QList<QString>’ has no member named ‘reserve’

/nfs/Users/blowekamp/QtSDK/Desktop/Qt/474/gcc/include/QtCore/qdatastream.h: In function ‘QDataStream& operator>>(QDataStream&, QList<T>&) [with T = QString]’:
/nfs/Users/blowekamp/QtSDK/Desktop/Qt/474/gcc/include/QtCore/qstringlist.h:247:   instantiated from here
/nfs/Users/blowekamp/QtSDK/Desktop/Qt/474/gcc/include/QtCore/qdatastream.h:246: error: ‘class QList<QString>’ has no member named ‘reserve’

You have multiple Qt versions installed on your machine. Try removing the Qt version installed on the system.

libarchive.so: undefined reference to `SHA256_Update'

Linking CXX executable ../../../../../bin/MRMLLogicCxxTests
/home/benjaminlong/work/slicer/Slicer-SuperBuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `SHA256_Update'
/home/benjaminlong/work/slicer/Slicer-SuperBuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `SHA256_Final'
/home/benjaminlong/work/slicer/Slicer-SuperBuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `SHA256_Init'
/home/benjaminlong/work/slicer/Slicer-SuperBuild-Debug/LibArchive-install/lib/libarchive.so: undefined reference to `MD5_Init'

Solution: 

cd Slicer-SuperBuild
rm -rf LibArchive-*
make -j4

Details:

No rule to make target `/usr/lib/x86_64-linux-gnu/libGL.so'

See http://techtidings.blogspot.com/2012/01/problem-with-libglso-on-64-bit-ubuntu.html

X11 Window errors at start time

X Error: BadWindow (invalid Window parameter) 3
  Extension:    137 (Uknown extension)
  Minor opcode: 4 (Unknown request)
  Resource id:  0x4200199
X Error: BadWindow (invalid Window parameter) 3
  Extension:    137 (Uknown extension)
  Minor opcode: 4 (Unknown request)
  Resource id:  0x42001a6
X Error: BadWindow (invalid Window parameter) 3
  Extension:    137 (Uknown extension)
  Minor opcode: 4 (Unknown request)
  Resource id:  0x42001b3

Solution:

  • Reinstall Nvidia drivers (that also rewrite the xorg.conf file).

error C2061: syntax error : identifier 'ssize_t'

4>1>Compiling...
4>1>version.c
4>1>c:\chene\winbin64\slicer4\cmcurl\urldata.h(585) : error C2061: syntax error : identifier 'ssize_t'
4>1>c:\chene\winbin64\slicer4\cmcurl\urldata.h(593) : error C2365: 'fread' : redefinition; previous definition was 'function'
4>1>        C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\include\stdio.h(248) : see declaration of 'fread'
4>1>c:\chene\winbin64\slicer4\cmcurl\urldata.h(610) : error C2059: syntax error : '}'

Solution:

ld: framework not found QtWebKit

[...]
Linking CXX shared library libPythonQt.dylib
ld: framework not found QtWebKit
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[8]: *** [libPythonQt.dylib] Error 1
[...]

See Slicer issue #2860

Workaround:

Solution:

On MacOSX 10.8, CMake hangs forever

Issue: http://www.na-mic.org/Bug/view.php?id=2957

Solution: Use CMake build >= 2.8.10.20130220-g53b279. See http://www.cmake.org/files/dev/cmake-2.8.10.20130220-g53b279-Darwin-universal.tar.gz

Details:

CMake folks (Thanks Brad King :)) fixed an issue that was preventing the most recent nightly from being used to successfully compile Slicer. The fix has been tested and is known to work. Tomorrow nightly build of CMake and by extension the coming release of CMake 2.8.11 will work.

If you are curious about the details, check the commit message: 

http://cmake.org/gitweb?p=cmake.git;a=commitdiff;h=1df09e57 [^]

The associated CMake test have also been updated: 

http://cmake.org/gitweb?p=cmake.git;a=commitdiff;h=bff3d9ce [^]



On MacOSX 10.8/10.9 with XQuartz, 'X11/Xlib.h' file not found

Issue: http://www.na-mic.org/Bug/view.php?id=3405

Workaround: Build with -DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF

Tcl is required only for EMSegment module.

Details: See http://www.na-mic.org/Bug/view.php?id=3405

svn: E175002: Unable to connect to a repository at URL XXX

Issue: Cisco AnyConnect is installed with the "Web Security" option checked (default), which blocks Subversion checkouts even when inactive!

Solution: Uninstall and reinstall Cisco AnyConnect, deselecting the "Web Security" feature during install

CiscoAnyConnectInstallOptions.png

My antivirus software reports that files in my build directory are infected

Although usually antivirus software does not interfere with the build process, it is recommended to disable antivirus and search indexing for build directories to improve performance and minimize the chance of concurrent file access problems.

Visual Studio compiler crashes

  • If you use Visual Studio 2008, make sure Visual Studio 2008 service pack 1 is installed
  • Build Slicer in a short directory, for example source code in C:\S4, binary directory C:\S4D or C:\S4R

'QSslSocket' : is not a class or namespace name

This error message occurs if Slicer is configured to use SSL but Qt is built without SSL support.

Either set Slicer_USE_PYTHONQT_WITH_OPENSSL to OFF when configuring Slicer build in CMake, or build Qt with SSL support.

error: Missing Qt module QTWEBKIT

CMake Error at CMake/SlicerBlockFindQtAndCheckVersion.cmake:43 (message):
 error: Missing Qt module QTWEBKIT
Call Stack (most recent call first):
 CMake/SlicerBlockFindQtAndCheckVersion.cmake:88 (__SlicerBlockFindQtAndCheckVersion_find_qt)
 CMakeLists.txt:607 (include)

Solution: 

sudo apt-get -y install libqtwebkit-dev

Details:

error when starting Slicer: NameError: name 'getSlicerRCFileName' is not defined

./Slicer Traceback (most recent call last): 

 File "<string>", line 7, in <module>
 File "/home/fbudin/Devel/Slicer-SuperBuild-Release/Slicer-build/bin/Python/slicer/slicerqt.py", line 6, in <module>
   import vtk
 File "/home/fbudin/Devel/Slicer-SuperBuild-Release/VTKv7-build/Wrapping/Python/vtk/__init__.py", line 41, in <module>
   from .vtkCommonKit import *
 File "/home/fbudin/Devel/Slicer-SuperBuild-Release/VTKv7-build/Wrapping/Python/vtk/vtkCommonKit.py", line 9, in <module>
   from vtkCommonKitPython import *

ImportError: /home/fbudin/Devel/Slicer-SuperBuild-Release/VTKv7-build/lib/./libvtkCommonKitPython27D-7.1.so.1: undefined symbol: PyUnicodeUCS2_DecodeUTF8 Traceback (most recent call last): 

 File "<string>", line 1, in <module>

NameError: name 'getSlicerRCFileName' is not defined Number of registered modules: 138 error: [/home/fbudin/Devel/Slicer-SuperBuild-Release/Slicer-build/bin/./SlicerApp-real] exit abnormally - Report the problem.

Solution and details here

macOS: error while configuring PCRE: "cannot run C compiled program"

If the XCode command line tools are not properly set up on OS X, PCRE could fail to build in the Superbuild process with the errors like below: 

configure: error: in `/Users/fedorov/local/Slicer4-Debug/PCRE-build':
configure: error: cannot run C compiled programs.

To install XCode command line tools, use the following command from the terminal: 

 xcode-select --install

Quick Build on Debian

sudo aptitude update
sudo aptitude install subversion git gcc g++ make cmake-curses-gui libqt4-dev
svn co http://svn.slicer.org/Slicer4/trunk Slicer
mkdir Slicer-SuperBuild-Debug
cd Slicer-SuperBuild-Debug
cmake ../Slicer
make -j5

# runtime dependency:
sudo aptitude install python-tk


Quick Build on Fedora 20

Thanks to Bill Lorensen, you will find below the instruction to quickly build Slicer on Fedora 20: 

yum groupinstall "C Development Tools"
yum install git-core
yum install svn
yum install libX11-devel
yum install libXt-devel
yum install mesa-libGL-devel
yum install mesa-libGLU-devel
yum install cmake
yum install tcl-devel
yum install python-devel
yum install qt-devel
yum install qt-webkit-devel

svn co http://svn.slicer.org/Slicer4/trunk Slicer
mkdir Slicer-SuperBuild-Debug
cd Slicer-SuperBuild-Debug
cmake ../Slicer
make -j5

Reference: http://slicer-devel.65872.n3.nabble.com/Fedora-20-Slicer-Experience-tt4030845.html

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