diff --git a/Calorimeter/CaloGeoHelpers/CMakeLists.txt b/Calorimeter/CaloGeoHelpers/CMakeLists.txt
index 1310aa65da8d5fef857662dd2039c6f94f7eea4b..9bee11c66a15f68ac5f8245b95f786d05b257b74 100644
--- a/Calorimeter/CaloGeoHelpers/CMakeLists.txt
+++ b/Calorimeter/CaloGeoHelpers/CMakeLists.txt
@@ -11,8 +11,6 @@ atlas_depends_on_subdirs( PUBLIC
                           PRIVATE
                           AtlasTest/TestTools )
 
-athena_install_nonstandard_headers(CaloGeoHelpers/CaloSampling.def)
-
 # Component(s) in the package:
 atlas_add_library( CaloGeoHelpers
                    Root/*.cxx
diff --git a/Event/xAOD/xAODCaloRings/CMakeLists.txt b/Event/xAOD/xAODCaloRings/CMakeLists.txt
index 099cc4d5935968d1a4bcbe5f775fbcb5e168de74..8ee53701c89227273d94f6cd091e0a8e2d7e754e 100644
--- a/Event/xAOD/xAODCaloRings/CMakeLists.txt
+++ b/Event/xAOD/xAODCaloRings/CMakeLists.txt
@@ -17,8 +17,6 @@ atlas_depends_on_subdirs( PUBLIC
 # External dependencies:
 find_package( ROOT COMPONENTS Core Tree MathCore Hist RIO pthread )
 
-athena_install_nonstandard_headers(xAODCaloRings/versions)
-
 # Component(s) in the package:
 atlas_add_library( xAODCaloRings
                    Root/*.cxx
diff --git a/InnerDetector/InDetConditions/PixelCoralClientUtils/CMakeLists.txt b/InnerDetector/InDetConditions/PixelCoralClientUtils/CMakeLists.txt
index 4b43a06419d87a9642342e5ca30a869a499fd96f..4503f63812e26341b05340690525ba8a1361caeb 100644
--- a/InnerDetector/InDetConditions/PixelCoralClientUtils/CMakeLists.txt
+++ b/InnerDetector/InDetConditions/PixelCoralClientUtils/CMakeLists.txt
@@ -14,8 +14,6 @@ find_package( COOL COMPONENTS CoolKernel )
 find_package( CORAL COMPONENTS CoralBase CoralKernel RelationalAccess )
 find_package( ROOT COMPONENTS Core Tree MathCore Hist RIO pthread )
 
-athena_install_nonstandard_headers(PixelCoralClientUtils/*.hh)
-
 # Component(s) in the package:
 atlas_add_library( PixelCoralClientUtils
                    src/CoralClient.cc
diff --git a/MuonSpectrometer/MuonCalib/MuonCalibUtils/MuonCalibMath/CMakeLists.txt b/MuonSpectrometer/MuonCalib/MuonCalibUtils/MuonCalibMath/CMakeLists.txt
index f805a3ffd98be028411944f493931d2e4444c9c8..d6238fd0d7a99c56efb4bad8ebabb8aa889d1afb 100644
--- a/MuonSpectrometer/MuonCalib/MuonCalibUtils/MuonCalibMath/CMakeLists.txt
+++ b/MuonSpectrometer/MuonCalib/MuonCalibUtils/MuonCalibMath/CMakeLists.txt
@@ -14,8 +14,6 @@ find_package( CLHEP )
 find_package( Eigen )
 find_package( ROOT COMPONENTS MathCore MathMore Core Tree Hist RIO pthread )
 
-athena_install_nonstandard_headers(MuonCalibMath/*.ixx)
-
 # Component(s) in the package:
 atlas_add_library( MuonCalibMath
                    src/*.cxx
diff --git a/PackDist/CMakeLists.txt b/PackDist/CMakeLists.txt
index 0dd46447e0b0779c34024098bacb6b2e531b898e..8da3a1343637f9f86fb1414591b36c86deb1a0c5 100644
--- a/PackDist/CMakeLists.txt
+++ b/PackDist/CMakeLists.txt
@@ -4,13 +4,3 @@
 
 # Declare the package name:
 atlas_subdir( PackDist )
-
-# this line failed automatic conversion in cmt2cmake :
-# set_remove PACKOPTS "-w"
-
-# this line failed automatic conversion in cmt2cmake :
-# set_append PACKOPTS " -w "
-
-athena_env( SET PACKCFG ../config/pack-nightly-bugfix.cfg
-            SET PACKOPTS \\\${PACKOPTS} )
-
diff --git a/Tools/CodeCheck/CMakeLists.txt b/Tools/CodeCheck/CMakeLists.txt
index 300e13e81e3743c9ae19817768627ade970dd41d..45fde9ae1508ede35c9b4b0db3d0511448139fb6 100644
--- a/Tools/CodeCheck/CMakeLists.txt
+++ b/Tools/CodeCheck/CMakeLists.txt
@@ -4,7 +4,3 @@
 
 # Declare the package name:
 atlas_subdir( CodeCheck )
-
-athena_env( SET atlas_checker_command \"\"
-            SET atlas_patch_command \"\" )
-
diff --git a/Tools/JobTransforms/CMakeLists.txt b/Tools/JobTransforms/CMakeLists.txt
index 842c57f41441ef04d6647ca3835b377907536f35..d7d8fedbbc6087973238ff57bfb52d6d99845d79 100644
--- a/Tools/JobTransforms/CMakeLists.txt
+++ b/Tools/JobTransforms/CMakeLists.txt
@@ -7,7 +7,3 @@ atlas_subdir( JobTransforms )
 
 # External dependencies:
 find_package( PythonLibs )
-
-athena_env( SET T_INCPATH \\\${CMTINSTALLAREA}/share/JT/include
-            SET T_RELEASE \\\${JobTransforms_project_release} )
-
diff --git a/Tools/Scripts/CMakeLists.txt b/Tools/Scripts/CMakeLists.txt
index 97ca5f0fe92665d72588d32701e237213f56d72a..c2bb7b08b7105059893ef399af5c4b1ed75805f0 100644
--- a/Tools/Scripts/CMakeLists.txt
+++ b/Tools/Scripts/CMakeLists.txt
@@ -5,12 +5,5 @@
 # Declare the package name:
 atlas_subdir( Scripts )
 
-# this line failed automatic conversion in cmt2cmake :
-# setup_script $(SETUPCOMPLETIONROOT)/cmt/completion/setup_completion_main
-
 # Install files from the package:
 atlas_install_scripts( share/get_joboptions share/get_files share/lookup_local_joboptions.sh share/lookup_joboptions.sh share/lookup_scripts.sh share/lookup_xmls.sh share/lookup_data.sh share/checkDbgSymbols.sh )
-
-athena_env( SET DO_EXT_ATHENA_TAB_COMPLETION 0
-            SET SETUPCOMPLETIONROOT \\\${SCRIPTSROOT} )
-
diff --git a/graphics/AtlantisJava/CMakeLists.txt b/graphics/AtlantisJava/CMakeLists.txt
index dbdecf499942302acba7d0e4a47917ac8321ada1..22a75316071acdb43709a945640765fb54c2c1e4 100644
--- a/graphics/AtlantisJava/CMakeLists.txt
+++ b/graphics/AtlantisJava/CMakeLists.txt
@@ -29,6 +29,3 @@ atlas_install_generic( geometry/*.xml
 atlas_install_generic( help/help.jar help/online.xml help/*.png
                        DESTINATION "share/AtlantisJava/help"
                        EXECUTABLE )
-
-athena_env( SET ANT_OPTS "-Xms64m -Xmx64m" )
-