diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
index 669d22ea580..dde92ba44d6 100644
--- a/doc/Doxyfile.in
+++ b/doc/Doxyfile.in
@@ -291,7 +291,7 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 # Note that for custom extensions you also need to set FILE_PATTERNS otherwise
 # the files are not read by doxygen.
 
-EXTENSION_MAPPING      = f90=FortranFree,F90=FortranFree 
+EXTENSION_MAPPING      = f90=FortranFree
 
 # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable
diff --git a/src/flib/piolib_mod.F90 b/src/flib/piolib_mod.F90
index 1d7d405c356..7c4ad1ff011 100644
--- a/src/flib/piolib_mod.F90
+++ b/src/flib/piolib_mod.F90
@@ -504,7 +504,6 @@ end subroutine PIO_initdecomp_bc
 !! @ingroup PIO_initdecomp
 !! @brief A deprecated interface to the PIO_initdecomp method.
 !! @details
-!! @deprecated
 !! @param iosystem : a defined pio system descriptor, see PIO_types
 !! @param basepiotype : the type of variable(s) associated with this iodesc.
 !! @copydoc PIO_kinds
@@ -514,6 +513,7 @@ end subroutine PIO_initdecomp_bc
 !! @param iodofr :
 !! @param iodofw :
 !! @param iodesc @copydoc iodesc_generate
+!! @deprecated
 !<
   subroutine initdecomp_2dof_bin_i4(iosystem,basepiotype,dims,lenblocks,compdof,iodofr,iodofw,iodesc)
     type (iosystem_desc_t), intent(in) :: iosystem
@@ -604,7 +604,6 @@ end subroutine initdecomp_1dof_bin_i4
 !! @ingroup PIO_initdecomp
 !! @brief A deprecated interface to the PIO_initdecomp method.
 !! @details
-!! @deprecated
 !! @param iosystem : a defined pio system descriptor, see PIO_types
 !! @param basepiotype : the type of variable(s) associated with this iodesc.
 !! @copydoc PIO_kinds
@@ -616,6 +615,7 @@ end subroutine initdecomp_1dof_bin_i4
 !! @param start : used with count to give a block description of the shape of the data
 !! @param count :
 !! @param iodesc @copydoc iodesc_generate
+!! @deprecated
 !<
   subroutine initdecomp_2dof_nf_i4(iosystem,basepiotype,dims,lenblocks,compdof,iodofr,iodofw,start, count, iodesc)
     type (iosystem_desc_t), intent(in) :: iosystem
@@ -664,7 +664,6 @@ end subroutine initdecomp_2dof_nf_i8
 !! @ingroup PIO_initdecomp
 !! @brief A deprecated interface to the PIO_initdecomp method.
 !! @details
-!! @deprecated
 !! @param iosystem : a defined PIO system descriptor, see pio_types
 !! @param basepiotype : The type of variable(s) associated with this iodesc.
 !! @copydoc PIO_kinds
@@ -675,6 +674,7 @@ end subroutine initdecomp_2dof_nf_i8
 !! @param start :
 !! @param count :
 !! @param iodesc @copydoc iodesc_generate
+!! @deprecated
 !<
   subroutine initdecomp_1dof_nf_i4(iosystem,basepiotype,dims,lenblocks,compdof,iodof,start, count, iodesc)
     type (iosystem_desc_t), intent(in) :: iosystem