Addressed comments and try sth else for cmake on travis.

Author: Julianus Pfeuffer

.travis.yml

@@ -8,7 +8,10 @@ addons:
       sources:
          - ubuntu-toolchain-r-test
          - boost-latest
+         - george-edison55-precise-backports
       packages:
+         - cmake
+         - cmake-data
          - g++-4.8
          - libboost-chrono1.55-dev
          - libboost-date-time1.55-dev

cmake/setup_lib_find_paths.cmake

@@ -39,16 +39,17 @@
 #------------------------------------------------------------------------------
 
 #------------------------------------------------------------------------------
-# emit warning if CMAKE_FIND_ROOT_PATH is used instead of CMAKE_PREFIX_PATH
-if(NOT "${CMAKE_FIND_ROOT_PATH}" STREQUAL "" AND "${CMAKE_PREFIX_PATH}" STREQUAL "")
-  set(CMAKE_PREFIX_PATH "${CMAKE_FIND_ROOT_PATH}")
-  message(STATUS "Please use CMAKE_PREFIX_PATH instead of CMAKE_FIND_ROOT_PATH ")
+# Specify the path to the contrib-build. Will be added to CMAKE_PREFIX_PATH
+# for searching and as first entry in the includes/libraries to avoid
+# mismatches with installed system libraries
+if(NOT OPENMS_CONTRIB_LIBS)
+  message(WARNING "Unless you are certain that you have all contributing libraries in system paths, please specify an explicit path to the built contrib libraries via
+-DOPENMS_CONTRIB_LIBS")
+else()
+  list(INSERT CMAKE_PREFIX_PATH 0 ${OPENMS_CONTRIB_LIBS})
+  list(REMOVE_DUPLICATES CMAKE_PREFIX_PATH)
 endif()
 
-#------------------------------------------------------------------------------
-# add contrib location of source package <source>/contrib
-list(APPEND CMAKE_PREFIX_PATH ${OPENMS_HOST_DIRECTORY}/contrib/)
-
 #------------------------------------------------------------------------------
 # Ensure Qt includes it's libs as SYSTEM
 set(QT_INCLUDE_DIRS_NO_SYSTEM Off)

doc/doxygen/install/install-linux.doxygen

@@ -189,7 +189,6 @@
   <tt>HAS_XSERVER=Off</tt>, especially as you may not have compiled Qt with
   OpenGL and you may not have an X server.
   If you want to use your own qt installation, be sure to set the <tt>QT_QMAKE_EXECUTABLE=/path/to/qmake</tt> flag when using cmake to configure %OpenMS.
-  Finally, you may have to remove any system libraries from the <tt>CMAKE_PREFIX_PATH</tt> to ensure that the correct version of each library is used.
 
   @section install_linux_openms Configuring and building OpenMS/TOPP
 
@@ -216,9 +215,15 @@
   <tt>/usr;/usr/local</tt> part of the path:
 
   \code
-  cmake -DCMAKE_PREFIX_PATH="/PATH/TO/contrib-build;/usr;/usr/local" -DBOOST_USE_STATIC=OFF ../OpenMS
+  cmake -DOPENMS_CONTRIB_LIBS="/PATH/TO/contrib-build" -DBOOST_USE_STATIC=OFF ../OpenMS
   \endcode
 
+  If CMake has problems finding system libraries, you might consider adding:
+  \code
+  -DCMAKE_PREFIX_PATH="/usr;/usr/local"
+  \endcode
+  to the CMake options.
+
   In order to <i>build</i> the %OpenMS library, the TOPP tools, tests, and this
   documentation, execute the following command:
 
@@ -304,14 +309,18 @@
           <BR>
           <b>Note:</b> Moving these directories after installing is not supported.
 
-	<b>For development, install prefixes are not supported. In this case %OpenMS must
-	be built in place!</b>
+	        <b>For development, install prefixes are not supported. In this case %OpenMS must
+	         be built in place!</b>
      </td>
     </tr>
+    <tr>
+      <td valign="top">\c OPENMS_CONTRIB_LIBS</td>
+      <td>Seperate search path for the contrib libraries from github.com/OpenMS/contrib that is internally considered before
+      CMAKE_PREFIX_PATH for searching, linking and adding include directories.</td>
+    </tr>
     <tr>
       <td valign="top">\c CMAKE_PREFIX_PATH</td>
-      <td>Additional search path for the contrib libraries.
-          If not set the location is assumed to be <pre>contrib/</pre> as packaged in the Release tar.gz.</td>
+      <td>Additional search path for the contrib libraries.</td>
     </tr>
     <tr>
       <td valign="top">\c QT_QMAKE_EXECUTABLE</td>

doc/doxygen/install/install-macs.doxygen

@@ -186,7 +186,7 @@
 
         \code
         cd <path_to_OpenMS_build>
-        cmake -DCMAKE_PREFIX_PATH=<path_to_contrib_build> <path_to_OpenMS>
+        cmake -DOPENMS_CONTRIB_LIBS=<path_to_contrib_build> <path_to_OpenMS>
         \endcode
 
       You can set CMake variables using the <code>-DVARIABLE=VALUE</code> option.
@@ -204,20 +204,34 @@
   The most important CMake variables are:
 
   <table style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;">
+    <tr>
+      <td valign="top">\c CMAKE_INSTALL_PREFIX</td>
+      <td>the path where the bin/ and lib/ directories should be installed to
+          (when <pre>sudo make install</pre> is wished for a system-wide
+          install: e.g. -DCMAKE_INSTALL_PREFIX=/usr/local/)
+          <BR>
+          <b>Note:</b> Moving these directories after installing is not supported.
+
+          <b>For development, install prefixes are not supported. In this case %OpenMS must
+           be built in place!</b>
+     </td>
+    </tr>
+    <tr>
+      <td valign="top">\c OPENMS_CONTRIB_LIBS</td>
+      <td>Seperate search path for the contrib libraries from github.com/OpenMS/contrib that is internally considered before
+      CMAKE_PREFIX_PATH for searching, linking and adding include directories.</td>
+    </tr>
     <tr>
       <td valign="top">\c CMAKE_PREFIX_PATH</td>
       <td>Additional search path for the contrib libraries.
-          If not set the the location is assumed to be
-          <tt>&lt;path_to_OpenMS&gt;/contrib</tt>.
           If you want to use libraries installed via Homebrew or MacPorts you might
           need to provide the corresponding paths
 
           <code>-DCMAKE_PREFIX_PATH=/usr/local/Cellar</code> for Homebrew
           <code>-DCMAKE_PREFIX_PATH=/opt/local</code> for MacPorts
 
           Please keep in mind that both Homebrew and MacPorts do not provide all libraries so
-          you also need to specify the path to your self-build contrib.
-          <code>-DCMAKE_PREFIX_PATH="/opt/local;~/openms-development/contrib-build"</code>
+          you also need to specify the path to your self-build contrib via -DOPENMS_CONTRIB_LIBS
       </td>
     </tr>
     <tr>

doc/doxygen/install/install-win.doxygen

@@ -38,7 +38,7 @@
             otherwise VS might crash during the compilation of the contrib package.
         <br><b>Not supported are MinGW (g++ based compiler) and VS2003 (and earlier). Do not use a MinGW-enabled shell since CMake will get confused!</b>
             Other compilers which are close to the VS toolchain might work, but are not tested.
-      <li>Have CMake 2.8.10 or greater installed (see http://www.cmake.org).<br>
+      <li>Have CMake 3.0.2 or greater installed (see http://www.cmake.org).<br>
 	      CMake's Generator (-G flag) must support your version of Visual Studio.<br>
           [VS2012 requires CMake 2.8.10 or later, VS2013 needs CMake 2.8.11.2, etc...]
       <li>To extract archives within submodules of the contrib you will need <tt>7-Zip</tt> (see http://www.7-zip.org/)
@@ -217,15 +217,15 @@
       <li>Call CMake to create the build system
         \code
         cd <path_to_OpenMS_build>
-        cmake -D CMAKE_PREFIX_PATH="<path_to_contrib_build>" -G "<generator>" "<path_to_OpenMS>"
+        cmake -D OPENMS_CONTRIB_LIBS="<path_to_contrib_build>" -G "<generator>" "<path_to_OpenMS>"
         \endcode
 
         The choice of <tt>&lt;generator&gt;</tt> is dependent on your system. Type <tt>cmake</tt> to see a list of available generators.
         @note We strongly recommend the Visual Studio Generator and it should be identical to the one used for building the contrib. Other generators (such as nmake) are not tested! If you need compiling on the command line, you can use <tt>msbuild</tt> also on VS solution files!
         Example:
         \code
         cd c:\dev\OpenMS_Win64
-        cmake -D CMAKE_PREFIX_PATH="C:\dev\contrib_win64_build" -G "Visual Studio 9 2008 Win64" ..\OpenMS
+        cmake -D OPENMS_CONTRIB_LIBS="C:\dev\contrib_win64_build" -G "Visual Studio 9 2008 Win64" ..\OpenMS
         \endcode
     </ol>
 

src/openms/CMakeLists.txt

@@ -108,15 +108,22 @@ if (WITH_CRAWDAD)
   list(APPEND OPENMS_DEP_LIBRARIES ${Crawdad_LIBRARY})
 endif()
 
+list(REMOVE_DUPLICATES OPENMS_DEP_LIBRARIES)
+
+set (OPENMS_CONTRIB_INCLUDE_DIRS "")
+if (OPENMS_CONTRIB_LIBS)
+ set (OPENMS_CONTRIB_INCLUDE_DIRS ${OPENMS_CONTRIB_LIBS}/include)
+endif()
+
 openms_add_library(TARGET_NAME  OpenMS
                    SOURCE_FILES  ${OpenMS_sources}
                    HEADER_FILES  ${OpenMS_sources_h}
                                  ${OpenMS_configured_headers}
                    INTERNAL_INCLUDES ${CMAKE_CURRENT_SOURCE_DIR}/include
                                      ${CMAKE_CURRENT_BINARY_DIR}/include
-									 PRIVATE_INCLUDES ${EOL_BSPLINE_INCLUDE_DIRECTORY}
-                   EXTERNAL_INCLUDES ${QT_INCLUDES}
-                                     ${GSL_INCLUDE_DIRS}
+		               PRIVATE_INCLUDES ${EOL_BSPLINE_INCLUDE_DIRECTORY}
+                   EXTERNAL_INCLUDES ${OPENMS_CONTRIB_INCLUDE_DIRS}
+                                     ${QT_INCLUDES}
                                      ${Boost_INCLUDE_DIRS}
                                      ${SEQAN_INCLUDE_DIRS}
                                      ${SQLITE_INCLUDE_DIR}

tools/travis/lnx-cibuild.before.sh

@@ -1,11 +1,5 @@
 #!/bin/bash
 
-mkdir cmake_tmp
-cd cmake_tmp
-wget --no-check-certificate https://cmake.org/files/v3.0/cmake-3.0.2-Linux-i386.tar.gz
-tar xf cmake-3.0.2-Linux-i386.tar.gz
-sudo cp -r cmake-3.0.2-Linux-i386/* /usr
-
 function build_contrib {
   cmake . -DBUILD_TYPE=$1