diff --git a/InnerDetector/InDetDetDescr/PixelGeoModelXml/CMakeLists.txt b/InnerDetector/InDetDetDescr/PixelGeoModelXml/CMakeLists.txt
index 767118d225c3af1cdbcec4e3fb05a0e8635f8727..ceffa48c08f05b6e894f2e446e72648086e18ba8 100644
--- a/InnerDetector/InDetDetDescr/PixelGeoModelXml/CMakeLists.txt
+++ b/InnerDetector/InDetDetDescr/PixelGeoModelXml/CMakeLists.txt
@@ -1,49 +1,22 @@
-################################################################################
-# Package: PixelGeoModelXml
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( PixelGeoModelXml )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          Control/AthenaKernel
-                          Database/AthenaPOOL/RDBAccessSvc
-                          DetectorDescription/GeoModelXml
-			  DetectorDescription/GeoModel/GeoModelUtilities
-                          GaudiKernel
-                          InnerDetector/InDetDetDescr/InDetGeoModelUtils
-                          InnerDetector/InDetDetDescr/PixelReadoutGeometry
-                          InnerDetector/InDetDetDescr/PixelReadoutGeometry
-                          InnerDetector/InDetDetDescr/InDetReadoutGeometry
-                          InnerDetector/InDetSimEvent
-                          PRIVATE
-                          Control/CLIDSvc
-                          Control/SGTools
-                          Control/StoreGate
-                          Database/AthenaPOOL/AthenaPoolUtilities
-                          DetectorDescription/DetDescrCond/DetDescrConditions
-                          DetectorDescription/GeoModel/GeoModelInterfaces
-                          DetectorDescription/GeometryDBSvc
-                          DetectorDescription/Identifier
-                          InnerDetector/InDetDetDescr/InDetIdentifier
-			  Tools/PathResolver )
-
 # External dependencies:
-find_package( Boost COMPONENTS filesystem thread system )
-find_package( CORAL COMPONENTS CoralBase CoralKernel RelationalAccess )
+find_package( GeoModelCore )
 
 # Component(s) in the package:
 atlas_add_library( PixelGeoModelXmlLib
                    src/*.cxx
                    PUBLIC_HEADERS PixelGeoModelXml
-                   INCLUDE_DIRS ${Boost_INCLUDE_DIRS} ${CORAL_INCLUDE_DIRS} 
-                   LINK_LIBRARIES ${Boost_LIBRARIES} ${CORAL_LIBRARIES} AthenaKernel GeoModelXml GeoModelUtilities GaudiKernel InDetGeoModelUtils InDetReadoutGeometry PixelReadoutGeometry PixelReadoutGeometry StoreGateLib InDetSimEvent
-                   PRIVATE_LINK_LIBRARIES SGTools AthenaPoolUtilities DetDescrConditions Identifier InDetIdentifier PathResolver)
+                   PRIVATE_INCLUDE_DIRS ${GEOMODELCORE_INCLUDE_DIRS}
+                   LINK_LIBRARIES GaudiKernel GeoModelUtilities GeoModelXml InDetGeoModelUtils PixelReadoutGeometry
+                   PRIVATE_LINK_LIBRARIES ${GEOMODELCORE_LIBRARIES} AthenaPoolUtilities DetDescrConditions GeoModelInterfaces GeometryDBSvcLib InDetReadoutGeometry InDetSimEvent PathResolver RDBAccessSvcLib SGTools StoreGateLib )
 
 atlas_add_component( PixelGeoModelXml
-		     src/components/*.cxx
-		     LINK_LIBRARIES SGTools StoreGateLib SGtests AthenaPoolUtilities DetDescrConditions Identifier InDetIdentifier PixelGeoModelXmlLib )
+                     src/components/*.cxx
+		             LINK_LIBRARIES PixelGeoModelXmlLib )
                      
 # Install files from the package:
-atlas_install_python_modules( python/*.py )
+atlas_install_python_modules( python/*.py POST_BUILD_CMD ${ATLAS_FLAKE8} )
diff --git a/PhysicsAnalysis/Algorithms/JetAnalysisAlgorithms/CMakeLists.txt b/PhysicsAnalysis/Algorithms/JetAnalysisAlgorithms/CMakeLists.txt
index 7bb96fef87b52c85dbae5d1ed8185b9d1e55d37d..360fcb5bc919a3f96d5820e396862f8a1299c2ef 100644
--- a/PhysicsAnalysis/Algorithms/JetAnalysisAlgorithms/CMakeLists.txt
+++ b/PhysicsAnalysis/Algorithms/JetAnalysisAlgorithms/CMakeLists.txt
@@ -1,29 +1,15 @@
-# Copyright (C) 2002-2018 CERN for the benefit of the ATLAS collaboration
-#
-# @author Nils Krumnack
-
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # The name of the package:
 atlas_subdir( JetAnalysisAlgorithms )
 
-atlas_depends_on_subdirs(
-    PUBLIC
-    Event/xAOD/xAODJet
-    PhysicsAnalysis/Algorithms/SelectionHelpers
-    PhysicsAnalysis/Algorithms/SystematicsHandles
-    PhysicsAnalysis/D3PDTools/AnaAlgorithm
-    Reconstruction/Jet/JetCalibTools
-    Reconstruction/Jet/JetCPInterfaces
-    Reconstruction/Jet/JetInterface
-    Reconstruction/Jet/JetJvtEfficiency
-    Reconstruction/MET/METUtilities )
-
 atlas_add_library( JetAnalysisAlgorithmsLib
    JetAnalysisAlgorithms/*.h JetAnalysisAlgorithms/*.icc Root/*.cxx
    PUBLIC_HEADERS JetAnalysisAlgorithms
    LINK_LIBRARIES xAODJet SelectionHelpersLib SystematicsHandlesLib
    AnaAlgorithmLib JetCalibToolsLib JetInterface
-   JetCPInterfaces JetJvtEfficiencyLib JetAnalysisInterfacesLib METUtilitiesLib )
+   JetCPInterfaces JetAnalysisInterfacesLib
+   PRIVATE_LINK_LIBRARIES METUtilitiesLib xAODMuon )
 
 atlas_add_dictionary( JetAnalysisAlgorithmsDict
    JetAnalysisAlgorithms/JetAnalysisAlgorithmsDict.h
@@ -33,10 +19,11 @@ atlas_add_dictionary( JetAnalysisAlgorithmsDict
 if( NOT XAOD_STANDALONE )
    atlas_add_component( JetAnalysisAlgorithms
       src/*.h src/*.cxx src/components/*.cxx
-      LINK_LIBRARIES GaudiKernel JetAnalysisAlgorithmsLib )
+      LINK_LIBRARIES AnaAlgorithmLib JetAnalysisInterfacesLib JetCPInterfaces JetCalibToolsLib
+      JetInterface SelectionHelpersLib SystematicsHandlesLib xAODJet JetAnalysisAlgorithmsLib )
 endif()
 
-atlas_install_python_modules( python/*.py )
+atlas_install_python_modules( python/*.py POST_BUILD_CMD ${ATLAS_FLAKE8} )
 atlas_install_joboptions( share/*_jobOptions.py )
 atlas_install_scripts( share/*_eljob.py )
 
diff --git a/PhysicsAnalysis/Algorithms/MetAnalysisAlgorithms/CMakeLists.txt b/PhysicsAnalysis/Algorithms/MetAnalysisAlgorithms/CMakeLists.txt
index 6070963b23c23cea2ae1944b6538e22aa8e32a66..9a477cd5b260cc707be0e00cf7f4d31578ac7456 100644
--- a/PhysicsAnalysis/Algorithms/MetAnalysisAlgorithms/CMakeLists.txt
+++ b/PhysicsAnalysis/Algorithms/MetAnalysisAlgorithms/CMakeLists.txt
@@ -1,29 +1,13 @@
-# Copyright (C) 2002-2018 CERN for the benefit of the ATLAS collaboration
-#
-# @author Nils Krumnack
-
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # The name of the package:
 atlas_subdir( MetAnalysisAlgorithms )
 
-# The package's dependencies:
-atlas_depends_on_subdirs(
-   PUBLIC
-   Event/xAOD/xAODMissingET
-   PhysicsAnalysis/Algorithms/SystematicsHandles
-   PhysicsAnalysis/D3PDTools/AnaAlgorithm
-   PhysicsAnalysis/Interfaces/METInterface
-   Reconstruction/MET/METInterface
-   Reconstruction/MET/METUtilities
-   PRIVATE )
-
 atlas_add_library( MetAnalysisAlgorithmsLib
    MetAnalysisAlgorithms/*.h MetAnalysisAlgorithms/*.icc Root/*.cxx
    PUBLIC_HEADERS MetAnalysisAlgorithms
-   LINK_LIBRARIES xAODMissingET
-   SystematicsHandlesLib AnaAlgorithmLib METInterface
-   SelectionHelpersLib METUtilitiesLib
-   PRIVATE_LINK_LIBRARIES  )
+   LINK_LIBRARIES AnaAlgorithmLib METInterface SystematicsHandlesLib xAODBase xAODMissingET
+   PRIVATE_LINK_LIBRARIES METUtilitiesLib xAODEventInfo )
 
 atlas_add_dictionary( MetAnalysisAlgorithmsDict
    MetAnalysisAlgorithms/MetAnalysisAlgorithmsDict.h
@@ -33,10 +17,11 @@ atlas_add_dictionary( MetAnalysisAlgorithmsDict
 if( NOT XAOD_STANDALONE )
    atlas_add_component( MetAnalysisAlgorithms
       src/*.h src/*.cxx src/components/*.cxx
-      LINK_LIBRARIES GaudiKernel MetAnalysisAlgorithmsLib )
+      LINK_LIBRARIES AnaAlgorithmLib METInterface SystematicsHandlesLib xAODBase
+      xAODMissingET MetAnalysisAlgorithmsLib )
 endif()
 
-atlas_install_python_modules( python/*.py )
+atlas_install_python_modules( python/*.py POST_BUILD_CMD ${ATLAS_FLAKE8} )
 atlas_install_joboptions( share/*_jobOptions.py )
 atlas_install_scripts( share/*_eljob.py )
 
diff --git a/PhysicsAnalysis/HadronicRecoilData/CMakeLists.txt b/PhysicsAnalysis/HadronicRecoilData/CMakeLists.txt
index e33ad5ab911fd51c288c99e2b26556881d3dcf78..2e592e37b78d77c1b86bdd76a778d75abd027266 100644
--- a/PhysicsAnalysis/HadronicRecoilData/CMakeLists.txt
+++ b/PhysicsAnalysis/HadronicRecoilData/CMakeLists.txt
@@ -1,27 +1,14 @@
-################################################################################
-# Package: HadronicRecoilData
-################################################################################
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 
 # Declare the package name:
 atlas_subdir( HadronicRecoilData )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PUBLIC
-                          Calorimeter/CaloEvent
-                          Control/AthenaKernel
-                          Control/AthContainers
-                          PhysicsAnalysis/TruthParticleID/McParticleEvent
-                          Reconstruction/MuonIdentification/muonEvent
-                          Reconstruction/Particle
-                          Reconstruction/egamma/egammaEvent )
-
 # External dependencies:
-find_package( ROOT COMPONENTS Core Tree MathCore Hist RIO pthread )
+find_package( ROOT COMPONENTS Core MathCore )
 
 # Component(s) in the package:
 atlas_add_library( HadronicRecoilData
                    src/*.cxx
                    PUBLIC_HEADERS HadronicRecoilData
                    INCLUDE_DIRS ${ROOT_INCLUDE_DIRS}
-                   LINK_LIBRARIES ${ROOT_LIBRARIES} CaloEvent AthContainers McParticleEvent muonEvent Particle egammaEvent )
-
+                   LINK_LIBRARIES ${ROOT_LIBRARIES} CaloEvent AthContainers AthenaKernel McParticleEvent muonEvent Particle egammaEvent )
diff --git a/Trigger/TriggerCommon/TriggerMenuXML/CMakeLists.txt b/Trigger/TriggerCommon/TriggerMenuXML/CMakeLists.txt
index d5fbba6c2368d67e67b5642219865ab23607f072..d2f5c01ccd9885fb215c9c55cc49e2c327c1cb79 100644
--- a/Trigger/TriggerCommon/TriggerMenuXML/CMakeLists.txt
+++ b/Trigger/TriggerCommon/TriggerMenuXML/CMakeLists.txt
@@ -1,3 +1,4 @@
+# Copyright (C) 2002-2020 CERN for the benefit of the ATLAS collaboration
 ################################################################################
 # Package: TriggerMenuXML
 ################################################################################
@@ -14,11 +15,6 @@
 # Declare the package name:
 atlas_subdir( TriggerMenuXML )
 
-# Declare the package's dependencies:
-atlas_depends_on_subdirs( PRIVATE
-                          Trigger/TriggerCommon/TriggerJobOpts
-                          Trigger/TriggerCommon/TriggerMenu )
-
 # Function to build trigger menu:
 function( atlas_build_trigger_menu menu )