diff --git a/biology/ncbi-vdb/Makefile b/biology/ncbi-vdb/Makefile
index 99f88f4f7131..a5d0c8811989 100644
--- a/biology/ncbi-vdb/Makefile
+++ b/biology/ncbi-vdb/Makefile
@@ -34,6 +34,7 @@ CONFIGURE_ARGS=	--with-xml2-prefix=${LOCALBASE} \
 		--with-hdf5-prefix=${LOCALBASE} \
 		--with-mbedtls-prefix=${LOCALBASE} \
 		CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
+MAKE_ENV+=	CPATH="${LOCALBASE}/include/libepoll-shim"
 MAKE_ARGS+=	CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
 
 CFLAGS+=	-I${WRKSRC}/lib
diff --git a/biology/ncbi-vdb/files/patch-libs_kns_linux_syspoll.c b/biology/ncbi-vdb/files/patch-libs_kns_linux_syspoll.c
deleted file mode 100644
index 4ed159f5e812..000000000000
--- a/biology/ncbi-vdb/files/patch-libs_kns_linux_syspoll.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- libs/kns/linux/syspoll.c.orig	2021-04-12 05:19:32 UTC
-+++ libs/kns/linux/syspoll.c
-@@ -43,7 +43,7 @@
- #include <unistd.h>
- #include <errno.h>
- 
--#include <sys/epoll.h>
-+#include <libepoll-shim/sys/epoll.h>
- #include <sys/types.h>
- #include <sys/socket.h>
- 
diff --git a/devel/libepoll-shim/Makefile b/devel/libepoll-shim/Makefile
index 4007bd093b54..d5ad62c3e276 100644
--- a/devel/libepoll-shim/Makefile
+++ b/devel/libepoll-shim/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	libepoll-shim
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.0.20210322
+DISTVERSION=	0.0.20210418
 CATEGORIES=	devel
 
 MAINTAINER=	x11@FreeBSD.org
diff --git a/devel/libepoll-shim/distinfo b/devel/libepoll-shim/distinfo
index 4812dda227ab..e1e49934cd93 100644
--- a/devel/libepoll-shim/distinfo
+++ b/devel/libepoll-shim/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1616417046
-SHA256 (jiixyj-epoll-shim-v0.0.20210322_GH0.tar.gz) = 5b8809f4d0f6c0cae1879b936fa98f4f219f3bf30656f4d1de403811e401bb0f
-SIZE (jiixyj-epoll-shim-v0.0.20210322_GH0.tar.gz) = 86359
+TIMESTAMP = 1618774132
+SHA256 (jiixyj-epoll-shim-v0.0.20210418_GH0.tar.gz) = 10d5ff1f4389e121fa2a07e0873eb61030ae655af9fd6980661eaa7fbb682b06
+SIZE (jiixyj-epoll-shim-v0.0.20210418_GH0.tar.gz) = 91936
diff --git a/devel/libepoll-shim/pkg-plist b/devel/libepoll-shim/pkg-plist
index 1ceb375cbad3..c8b071aea53a 100644
--- a/devel/libepoll-shim/pkg-plist
+++ b/devel/libepoll-shim/pkg-plist
@@ -1,3 +1,7 @@
+include/libepoll-shim/epoll-shim/detail/common.h
+include/libepoll-shim/epoll-shim/detail/poll.h
+include/libepoll-shim/epoll-shim/detail/read.h
+include/libepoll-shim/epoll-shim/detail/write.h
 include/libepoll-shim/sys/epoll.h
 %%SHIM_EVENTFD%%include/libepoll-shim/sys/eventfd.h
 include/libepoll-shim/sys/signalfd.h
diff --git a/graphics/wayland/files/patch-tests_os-wrappers-test.c b/graphics/wayland/files/patch-tests_os-wrappers-test.c
index afcae14b9d2e..e58d75ba56fd 100644
--- a/graphics/wayland/files/patch-tests_os-wrappers-test.c
+++ b/graphics/wayland/files/patch-tests_os-wrappers-test.c
@@ -9,7 +9,7 @@
  #include <stdlib.h>
  #include <stdint.h>
  #include <assert.h>
-@@ -73,10 +75,12 @@ socket(int domain, int type, int protocol)
+@@ -73,15 +75,22 @@ socket(int domain, int type, int protocol)
  {
  	wrapped_calls_socket++;
  
@@ -22,7 +22,17 @@
  
  	return real_socket(domain, type, protocol);
  }
-@@ -89,10 +93,12 @@ fcntl(int fd, int cmd, ...)
+ 
+ __attribute__ ((visibility("default"))) int
++#ifdef fcntl
++/* Work around #define fcntl in epoll-shim */
++#define old_fcntl fcntl
++#undef fcntl
++#endif
+ fcntl(int fd, int cmd, ...)
+ {
+ 	va_list ap;
+@@ -89,10 +98,12 @@ fcntl(int fd, int cmd, ...)
  
  	wrapped_calls_fcntl++;
  
@@ -35,7 +45,16 @@
  
  	va_start(ap, cmd);
  	arg = va_arg(ap, void*);
-@@ -106,10 +112,12 @@ recvmsg(int sockfd, struct msghdr *msg, int flags)
+@@ -100,16 +111,21 @@ fcntl(int fd, int cmd, ...)
+ 
+ 	return real_fcntl(fd, cmd, arg);
+ }
++#ifdef old_fcntl
++#define fcntl old_fcntl 
++#endif
+ 
+ __attribute__ ((visibility("default"))) ssize_t
+ recvmsg(int sockfd, struct msghdr *msg, int flags)
  {
  	wrapped_calls_recvmsg++;
  
@@ -48,7 +67,7 @@
  
  	return real_recvmsg(sockfd, msg, flags);
  }
-@@ -156,12 +164,14 @@ TEST(os_wrappers_socket_cloexec)
+@@ -156,12 +172,14 @@ TEST(os_wrappers_socket_cloexec)
  	do_os_wrappers_socket_cloexec(0);
  }
  
@@ -63,7 +82,7 @@
  
  static void
  do_os_wrappers_dupfd_cloexec(int n)
-@@ -195,11 +205,13 @@ TEST(os_wrappers_dupfd_cloexec)
+@@ -195,11 +213,13 @@ TEST(os_wrappers_dupfd_cloexec)
  	do_os_wrappers_dupfd_cloexec(0);
  }
  
@@ -77,7 +96,7 @@
  
  struct marshal_data {
  	struct wl_connection *read_connection;
-@@ -218,8 +230,7 @@ struct marshal_data {
+@@ -218,8 +238,7 @@ struct marshal_data {
  static void
  setup_marshal_data(struct marshal_data *data)
  {
@@ -87,7 +106,7 @@
  
  	data->read_connection = wl_connection_create(data->s[0]);
  	assert(data->read_connection);
-@@ -328,11 +339,13 @@ TEST(os_wrappers_recvmsg_cloexec)
+@@ -328,11 +347,13 @@ TEST(os_wrappers_recvmsg_cloexec)
  	do_os_wrappers_recvmsg_cloexec(0);
  }