diff --git a/devel/RStudio/Makefile b/devel/RStudio/Makefile
index 961372fdf98a..8d04a06d90a9 100644
--- a/devel/RStudio/Makefile
+++ b/devel/RStudio/Makefile
@@ -1,142 +1,148 @@
 # This port opens too many files during build, more than the default setting.
-# Its build is known to succeed with MAX_FILES_RStudio=4096 and MAX_FILES_RStudio_server=4096 in poudriere.conf
+# Its build is known to succeed with MAX_FILES_RStudio=4096 in poudriere.conf
 
 PORTNAME=	RStudio
 DISTVERSIONPREFIX=	v
 DISTVERSION=	1.4.1717
+PORTREVISION=	3
 CATEGORIES=	devel math java
 MASTER_SITES=	https://s3.amazonaws.com/rstudio-buildtools/dictionaries/:dictionaries \
 		https://s3.amazonaws.com/rstudio-buildtools/:buildtools
 DISTFILES=	core-dictionaries.zip:dictionaries \
 		gin-${GIN_VERSION}.zip:buildtools \
 		gwt-${GWT_VERSION}.zip:buildtools \
 		mathjax-27.zip:buildtools
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Integrated development environment (IDE) for R
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 BROKEN_i386=	[ERROR] Line 101: Failed to resolve 'org.rstudio.studio.client.workbench.views.vcs.common.diff.LineActionButtonRenderer.GrayResources' via deferred binding
 
 BUILD_DEPENDS=	ant:devel/apache-ant \
 		${LOCALBASE}/include/sys/sysinfo.h:devel/libsysinfo \
 		node:www/node \
 		pandoc:textproc/hs-pandoc \
 		R-cran-rstudioapi>0:devel/R-cran-rstudioapi
 LIB_DEPENDS=	libR.so:math/R \
 		libboost_thread.so:devel/boost-libs \
 		libinotify.so:devel/libinotify \
 		libsoci_core.so:databases/soci \
 		libuuid.so:misc/e2fsprogs-libuuid \
 		libyaml-cpp.so:devel/yaml-cpp
 
 FLAVORS=	desktop server
 FLAVOR?=	${FLAVORS:[1]}
 server_PKGNAMESUFFIX=	-server
 
 USES=		cmake fortran localbase:ldflags pgsql pkgconfig sqlite ssl
 USE_JAVA=	yes
 JAVA_VERSION=	8
 JAVA_BUILD=	yes
 USE_GITHUB=	yes
 GH_PROJECT=	${PORTNAME:tl}
 GH_TUPLE=	rstudio:r2d3:v0.2.0:r2d3/dependencies/common/r2d3 \
 		rstudio:rmarkdown:aed26ac:rmarkdown/dependencies/common/rmarkdown \
 		rstudio:rsconnect:03c379b:rsconnect/dependencies/common/rsconnect \
 		trestletech:plumber:v0.4.6:plumber/dependencies/common/plumber
 
 CMAKE_ARGS=	-DFREEBSD_RSTUDIO_VERSION:STRING=${PORTVERSION} \
 		-DFREEBSD_LIBDIR:STRING=${PREFIX}/lib
 CMAKE_ARGS+=	-DQT_QMAKE_EXECUTABLE:STRING=${QMAKE}
 CMAKE_ARGS+=	-DRSTUDIO_BOOST_SIGNALS_VERSION=2
 CMAKE_ARGS+=	-DFREEBSD_PORT_VERSION:STRING=${DISTVERSION}
 CMAKE_ARGS+=	-DFREEBSD_LOCALBASE:STRING=${LOCALBASE} # SOCI package is looked up here, see patch patch-src_cpp_CMakeLists.txt
 CMAKE_ON=	RSTUDIO_USE_SYSTEM_YAML_CPP \
 		RSTUDIO_USE_SYSTEM_SOCI
 MAKE_ENV=	HOME=${WRKDIR} \
 		JAVA_HOME=${JAVA_HOME} \
 		PATH=${JAVA_HOME}/bin:${PATH} \
 		ANT_OPTS="-Duser.home=${WRKDIR}"
 
 GWT_VERSION=	2.8.1
 GIN_VERSION=	2.1.2
 
 .if ${FLAVOR:U} == desktop
 DEPRECATED=	Uses EOL Python 2.7 via www/qt5-webengine
 EXPIRATION_DATE=2021-06-23
 COMMENT+=	(desktop UI version)
 USES+=		desktop-file-utils qt:5 shared-mime-info
 USE_QT=		core dbus declarative gui location network opengl printsupport quickcontrols sensors \
 		sql svg webchannel webengine webkit widgets xml xmlpatterns buildtools_build qmake_build
 CMAKE_ARGS+=	-DRSTUDIO_TARGET=Desktop
 INSTALL_SUBDIR=	${PORTNAME:tl}
 EXECUTABLE=	${PORTNAME:tl}
 .endif
 
 .if ${FLAVOR:U} == server
 COMMENT+=	(web UI version)
 CMAKE_ARGS+=	-DRSTUDIO_TARGET=Server
 LDFLAGS+=	-linotify
 INSTALL_SUBDIR=	${PORTNAME:tl}-server
 EXECUTABLE=	rserver
 USER=		nobody
 SUB_LIST=	USER=${USER}
 USE_RC_SUBR=	${PORTNAME:tl}-server
 .endif
 
 post-extract:
 	@${MKDIR} ${WRKSRC}/dependencies/dictionaries && ${MV} ${WRKDIR}/en_* ${WRKSRC}/dependencies/dictionaries/
 	@${MV} ${WRKDIR}/mathjax-* ${WRKSRC}/dependencies/
 	@${MKDIR} ${WRKSRC}/src/gwt/lib/gwt && ${MV} ${WRKDIR}/gwt-${GWT_VERSION} ${WRKSRC}/src/gwt/lib/gwt/${GWT_VERSION}
 	@${MKDIR} ${WRKSRC}/src/gwt/lib/gin/${GIN_VERSION} && ${MV} ${WRKDIR}/*.jar ${WRKSRC}/src/gwt/lib/gin/${GIN_VERSION}/
 
 post-patch:
 	@${REINPLACE_CMD} -e ' \
 		s|target_link_libraries(rstudio|target_link_libraries(rstudio procstat|; \
 		s|get_filename_component|#get_filename_component|; \
 		s|set(CMAKE_PREFIX_PATH "$${QT_BIN_DIR}//..//lib//cmake")|set(CMAKE_PREFIX_PATH "${LOCALBASE}/lib/cmake")|; \
 		s|/usr/share/|${PREFIX}/share/|g' \
 		${WRKSRC}/src/cpp/desktop/CMakeLists.txt
 	@${REINPLACE_CMD} -e ' \
 		s|</java>|<jvmarg value="-Duser.home=${WRKDIR}"/></java>|' \
 		${WRKSRC}/src/gwt/build.xml
 	@${REINPLACE_CMD} -e ' \
 		s|rHomePaths.push_back|//rHomePaths.push_back|; \
 		s|//rHomePaths.push_back(FilePath("/usr/local/lib/|rHomePaths.push_back(FilePath("${PREFIX}/lib/|' \
 		${WRKSRC}/src/cpp/core/r_util/RVersionsPosix.cpp
 	@${REINPLACE_CMD} -e ' \
 		s|<condition property="node.bin" value="../../../$${node.dir}/bin/node">|<condition property="node.bin" value="${LOCALBASE}/bin/node">|' \
 		${WRKSRC}/src/gwt/build.xml
 
 pre-build:
 	@${CP} ${FILESDIR}/global-setenv.h ${WRKSRC}/src/cpp/desktop/
 	@${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' ${WRKSRC}/src/cpp/desktop/global-setenv.h
-	@${ECHO} "Current max open files (ulimit -n) setting is $$(ulimit -n)." # since build is likely to fail when it is lower than 4096
 
 post-install:
 	@(echo "#!/bin/sh"; \
 	  echo ""; \
 	  echo "if ! [ -d /proc/curproc ]; then"; \
 	  echo "  echo \"${PORTNAME} needs /proc to be mounted as procfs\" >&2"; \
 	  echo "  exit 1"; \
 	  echo "fi"; \
 	  echo ""; \
 	  echo "# workaround for the problem that RStudio passes /lib with LD_LIBRARY_PATH that causes the /lib/libgcc_s.so.1 conflict with gcc"; \
 	  echo "LD_PRELOAD=${PREFIX}/lib/gcc${GCC_DEFAULT}/libgcc_s.so JAVA_HOME=${JAVA_HOME} ${PREFIX}/lib/${INSTALL_SUBDIR}/bin/${EXECUTABLE} \"$$"@"\"" \
 	) > ${STAGEDIR}${PREFIX}/bin/${EXECUTABLE}
 	@${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${EXECUTABLE}
 .if ${FLAVOR:U} == desktop
 	${REINPLACE_CMD} -e 's|^Exec=.*/rstudio|Exec=${PREFIX}/bin/${EXECUTABLE}|' ${STAGEDIR}${PREFIX}/share/applications/${EXECUTABLE}.desktop
 .endif
 .if ${FLAVOR:U} == server
 	${RM} ${STAGEDIR}${LOCALBASE}/lib/${INSTALL_SUBDIR}/bin/rstudio-server # not compatible with FreeBSD
 .endif
 	# Some functions expect the pandoc symlink.
 	@${MKDIR} ${STAGEDIR}${PREFIX}/lib/${INSTALL_SUBDIR}/bin/pandoc
 	@cd ${STAGEDIR}${PREFIX}/lib/${INSTALL_SUBDIR}/bin/pandoc && ${LN} -s ../../../../bin/pandoc
+	# Add $LOCALBASE/bin to PATH to allow RStudio-server to run gmake (R_HOME/etc/Renviron.site is installed, see https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html)
+.if ${FLAVOR:U} == server
+	#@${MKDIR} ${STAGEDIR}${LOCALBASE}/lib/R/etc
+	#@${ECHO} "PATH=\"${LOCALBASE}/bin:\$$PATH\"" > ${STAGEDIR}${LOCALBASE}/lib/R/etc/Renviron.site # it should be this way, but this fails: https://github.com/rstudio/rstudio/issues/9815
+	@${LN} -s ${LOCALBASE}/bin/${GMAKE} ${STAGEDIR}${PREFIX}/lib/rstudio-server/bin/postback/${GMAKE} # hack, should be as above, but at least gmake is in the path now
+.endif
 	# There is a variability in .js file names due to use of random numbers, so we use the automatic plist.
 	@${SETENV} ${CO_ENV} ${SH} ${SCRIPTSDIR}/check-stagedir.sh makeplist | ${GREP} -v ^\/ | ${SED} -e 's|%%WWWDIR%%|www/rstudio| ; s|%%CMAKE_BUILD_TYPE%%|${CMAKE_BUILD_TYPE:tl}|' > ${TMPPLIST}
 
 .include <bsd.port.mk>
diff --git a/math/nauty/files/patch-makefile.in b/math/nauty/files/patch-makefile.in
new file mode 100644
index 000000000000..76dc49de9aac
--- /dev/null
+++ b/math/nauty/files/patch-makefile.in
@@ -0,0 +1,13 @@
+- allow to add additional CFLAGS to build shared libraries
+
+--- makefile.in.orig	2021-09-03 17:45:35 UTC
++++ makefile.in
+@@ -3,7 +3,7 @@
+ 
+ SHELL=@SHELL@
+ CC=@CC@
+-CFLAGS=@CFLAGS@ @MORECFLAGS@
++CFLAGS=@CFLAGS@ @MORECFLAGS@ ${FREEBSD_EXTRA_CFLAGS}
+ SAFECFLAGS=@CFLAGS@
+ LDFLAGS=@LDFLAGS@ @LIBS@
+ THREADLIB=@threadlib@