diff --git a/biology/cufflinks/files/patch-configure.ac b/biology/cufflinks/files/patch-configure.ac
index e40d507ff95b..5d8f553f27ad 100644
--- a/biology/cufflinks/files/patch-configure.ac
+++ b/biology/cufflinks/files/patch-configure.ac
@@ -1,6 +1,15 @@
---- configure.ac.orig	2019-05-29 06:53:24 UTC
+--- configure.ac.orig	2019-07-06 16:28:01 UTC
 +++ configure.ac
-@@ -77,9 +77,10 @@ case "${host_cpu}-${host_os}" in
+@@ -14,7 +14,7 @@ AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])
+ AC_CONFIG_SRCDIR([config.h.in])
+ AC_CONFIG_HEADERS([config.h])
+ AC_CONFIG_AUX_DIR([build-aux])
+-AM_INIT_AUTOMAKE
++AM_INIT_AUTOMAKE([-Wall tar-pax foreign])
+ 
+ #AM_PATH_CPPUNIT(1.10.2)
+ 
+@@ -78,9 +78,10 @@ case "${host_cpu}-${host_os}" in
  	AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
    *)
      AC_MSG_CHECKING([if gcc accepts -m64])
@@ -14,3 +23,11 @@
  esac
  
  AC_ARG_ENABLE(vectorize,    [  --enable-vectorize        Enable GCC auto-vectorization],
+@@ -120,7 +121,6 @@ LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
+ AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>])
+ AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>])
+ 
+-AM_INIT_AUTOMAKE([-Wall tar-pax foreign])
+ 
+ AC_CONFIG_FILES([Makefile				 
+ 				 src/Makefile])
diff --git a/biology/phyml/files/patch-configure.ac b/biology/phyml/files/patch-configure.ac
new file mode 100644
index 000000000000..c96d56cf91bc
--- /dev/null
+++ b/biology/phyml/files/patch-configure.ac
@@ -0,0 +1,10 @@
+--- configure.ac.orig	2020-07-09 11:49:16 UTC
++++ configure.ac
+@@ -10,7 +10,6 @@ AC_CONFIG_HEADERS([config.h])
+ AC_DEFINE([UNIX],[1],[Unix tag on])
+ AC_DEFINE([DEBUG],[1],[Debug tag on])
+ 
+-AM_INIT_AUTOMAKE
+ AC_CANONICAL_HOST
+ 
+ AC_PROG_CC([gcc])
diff --git a/devel/automake/Makefile b/devel/automake/Makefile
index 8d4c3a2e0b53..be929f4b81c5 100644
--- a/devel/automake/Makefile
+++ b/devel/automake/Makefile
@@ -1,7 +1,7 @@
 # Created by: Ade Lovett <ade@FreeBSD.org>
 
 PORTNAME=	automake
-PORTVERSION=	1.16.4
+PORTVERSION=	1.16.5
 CATEGORIES=	devel
 MASTER_SITES=	GNU
 
@@ -18,9 +18,8 @@ RUN_DEPENDS=	autoconf>=2.69:devel/autoconf
 
 BUILD_VERSION=	1.16
 PLIST_SUB=	BUILD_VERSION=${BUILD_VERSION}
-USES=		cpe makeinfo perl5 tar:xz
+USES=		cpe perl5 tar:xz
 GNU_CONFIGURE=	yes
-MAKE_ENV+=	MAKEINFOFLAGS=--no-split
 INFO=		automake automake-history
 CPE_VENDOR=	gnu
 
diff --git a/devel/automake/distinfo b/devel/automake/distinfo
index 8943b19ae556..004d7dc28c17 100644
--- a/devel/automake/distinfo
+++ b/devel/automake/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1629873306
-SHA256 (automake-1.16.4.tar.xz) = 80facc09885a57e6d49d06972c0ae1089c5fa8f4d4c7cfe5baea58e5085f136d
-SIZE (automake-1.16.4.tar.xz) = 1599336
+TIMESTAMP = 1638700499
+SHA256 (automake-1.16.5.tar.xz) = f01d58cd6d9d77fbdca9eb4bbd5ead1988228fdb73d6f7a201f5f8d6b118b469
+SIZE (automake-1.16.5.tar.xz) = 1601740
diff --git a/net/megacmd/files/patch-configure.ac b/net/megacmd/files/patch-configure.ac
new file mode 100644
index 000000000000..3afddc5237e0
--- /dev/null
+++ b/net/megacmd/files/patch-configure.ac
@@ -0,0 +1,19 @@
+--- configure.ac.orig	2021-03-23 04:49:30 UTC
++++ configure.ac
+@@ -37,7 +37,7 @@ m4_define([megacmd_lt_age], [0])
+ 
+ AC_INIT([MEGAcmd], m4_esyscmd([ grep define < src/megacmdversion.h | awk '{print $3}' | awk 'BEGIN { RS = "" ; FS = "\n" } {printf $1"."$2"."$3}']), [https://github.com/meganz/megacmd])
+ 
+-AM_INIT_AUTOMAKE
++AM_INIT_AUTOMAKE([1.11 foreign silent-rules])
+ 
+ AC_PROG_CC
+ AC_CONFIG_FILES(Makefile)
+@@ -50,7 +50,6 @@ AC_CONFIG_SUBDIRS(sdk)
+ # AC_GNU_SOURCE
+ AC_USE_SYSTEM_EXTENSIONS
+ 
+-AM_INIT_AUTOMAKE([1.11 foreign silent-rules])
+ AC_CONFIG_HEADERS([src/megacmdconfig.h]) #this avoids inline definitions of stuff already defined in sdk's config.h (e.g: -DPACKAGE_NAME)
+ 
+ LT_INIT([shared disable-static win32-dll])
diff --git a/www/e2guardian/files/patch-configure.ac b/www/e2guardian/files/patch-configure.ac
index f2ad869a4d4d..b1ac36942f56 100644
--- a/www/e2guardian/files/patch-configure.ac
+++ b/www/e2guardian/files/patch-configure.ac
@@ -1,6 +1,14 @@
---- configure.ac.orig	2018-08-21 08:17:02 UTC
+--- configure.ac.orig	2020-01-27 08:24:39 UTC
 +++ configure.ac
-@@ -617,7 +617,6 @@ else
+@@ -6,7 +6,6 @@ AC_DEFINE([FD_SETSIZE_OVERIDE],[""],[Define to allow D
+ 
+ AC_PREREQ(2.57)
+ AC_INIT(e2guardian, 5.3.4)
+-AM_INIT_AUTOMAKE
+ AC_CONFIG_HEADERS([dgconfig.h])
+ AC_CONFIG_MACRO_DIR([m4])
+ AM_INIT_AUTOMAKE([subdir-objects])
+@@ -617,7 +616,6 @@ else
  	AC_MSG_RESULT(yes)
  	dnsauth=true
  	DNSAUTHSUPPORT=""