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 @@ -1,64 +1,65 @@ PORTNAME= ncbi-vdb DISTVERSION= 2.11.0 PORTREVISION= 1 CATEGORIES= biology MAINTAINER= mzaki@niid.go.jp COMMENT= NCBI's virtualized back-end for accessing Sequence Read Archive LICENSE= PD LICENSE_FILE= ${WRKSRC}/LICENSE ONLY_FOR_ARCHS= amd64 i386 ONLY_FOR_ARCHS_REASON= libs/search/nucstrstr.c requires SSE2 instructions BUILD_DEPENDS= bash:shells/bash \ libepoll-shim>0:devel/libepoll-shim LIB_DEPENDS= libxml2.so:textproc/libxml2 \ libhdf5.so:science/hdf5 \ libmbedtls.so:security/mbedtls USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix USE_PERL5= build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ncbi GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs # ported as biology/ngs-sdk SHEBANG_GLOB= *.sh *.pl GNU_CONFIGURE= yes 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${WRKSRC}/lib MAKE_JOBS_UNSAFE= yes post-extract: @${LN} -sf ${WRKSRC_ngs} ${WRKDIR}/ngs @${LN} -sf ${WRKSRC} ${WRKDIR}/${PORTNAME} pre-patch: @${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/ @for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done @${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh @${MKDIR} ${WRKSRC}/interfaces/os/bsd @${CP} -p ${WRKSRC}/interfaces/os/mac/endian.h ${WRKSRC}/interfaces/os/bsd/ post-patch: @${GREP} -q '@@PREFIX@@' ${WRKSRC}/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1) @${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/libs/kfg/config.c post-configure: @${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP # The 'install' target installs broken-looking static libs with symlinks. # This is intentional, see comments https://github.com/ncbi/ncbi-vdb/issues/36#issuecomment-817990790 This may change in future versions. .include 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 - #include - --#include -+#include - #include - #include - 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 @@ -1,35 +1,35 @@ # Created by: Johannes Lundberg PORTNAME= libepoll-shim DISTVERSIONPREFIX= v -DISTVERSION= 0.0.20210322 +DISTVERSION= 0.0.20210418 CATEGORIES= devel MAINTAINER= x11@FreeBSD.org COMMENT= Small epoll implementation using kqueue LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake compiler:c11 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= jiixyj GH_PROJECT= epoll-shim PLIST_SUB= SHIM_EVENTFD="${exists(/usr/include/sys/eventfd.h):?@comment :}" do-test: # Exclude certain tests in resource restricted environments @(if [ `ulimit -n` -lt 20100 ]; then \ ${ECHO} "Skipping test perf-many-fds.perf_many_fds__perf"; \ SKIP_TESTS="-E ^(perf-many-fds.perf_many_fds__perf"; \ if [ `ulimit -n` -lt 1100 ]; then \ ${ECHO} "Skipping test timerfd-test.timerfd__many_timers"; \ SKIP_TESTS=$$SKIP_TESTS"|timerfd-test.timerfd__many_timers"; \ fi; \ SKIP_TESTS=$$SKIP_TESTS")$$"; \ fi; \ cd ${TEST_WRKSRC} && \ ${SETENV} ${TEST_ENV} ctest -C ${CMAKE_BUILD_TYPE} $$SKIP_TESTS) .include 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 @@ -1,10 +1,14 @@ +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 include/libepoll-shim/sys/timerfd.h lib/cmake/epoll-shim/epoll-shim-config.cmake lib/cmake/epoll-shim/epoll-shim-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/epoll-shim/epoll-shim-targets.cmake lib/libepoll-shim.so lib/libepoll-shim.so.0 libdata/pkgconfig/epoll-shim.pc 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 @@ -1,103 +1,122 @@ --- tests/os-wrappers-test.c.orig 2017-08-08 18:20:52 UTC +++ tests/os-wrappers-test.c @@ -26,6 +26,8 @@ #define _GNU_SOURCE +#include "../config.h" + #include #include #include -@@ -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++; +#ifdef SOCK_CLOEXEC if (fall_back && (type & SOCK_CLOEXEC)) { errno = EINVAL; return -1; } +#endif 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++; +#ifdef F_DUPFD_CLOEXEC if (fall_back && (cmd == F_DUPFD_CLOEXEC)) { errno = EINVAL; return -1; } +#endif 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++; +#ifdef MSG_CMSG_CLOEXEC if (fall_back && (flags & MSG_CMSG_CLOEXEC)) { errno = EINVAL; return -1; } +#endif 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); } +#ifdef SOCK_CLOEXEC TEST(os_wrappers_socket_cloexec_fallback) { /* forced fallback */ init_fallbacks(1); do_os_wrappers_socket_cloexec(1); } +#endif 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); } +#ifdef F_DUPFD_CLOEXEC TEST(os_wrappers_dupfd_cloexec_fallback) { init_fallbacks(1); do_os_wrappers_dupfd_cloexec(3); } +#endif 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) { - assert(socketpair(AF_UNIX, - SOCK_STREAM | SOCK_CLOEXEC, 0, data->s) == 0); + assert(wl_os_socketpair_cloexec(AF_UNIX, SOCK_STREAM, 0, data->s) == 0); 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); } +#ifdef MSG_CMSG_CLOEXEC TEST(os_wrappers_recvmsg_cloexec_fallback) { init_fallbacks(1); do_os_wrappers_recvmsg_cloexec(1); } +#endif static void do_os_wrappers_epoll_create_cloexec(int n)