Date: Wed, 1 Jan 2025 11:00:12 GMT From: Rene Ladan <rene@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 23a1c806a827 - main - biology/ncbi-vdb: Remove expired port Message-ID: <202501011100.501B0CD6023436@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by rene: URL: https://cgit.FreeBSD.org/ports/commit/?id=23a1c806a82791264e96eeccc9ad7926a1276316 commit 23a1c806a82791264e96eeccc9ad7926a1276316 Author: Rene Ladan <rene@FreeBSD.org> AuthorDate: 2025-01-01 10:59:57 +0000 Commit: Rene Ladan <rene@FreeBSD.org> CommitDate: 2025-01-01 10:59:57 +0000 biology/ncbi-vdb: Remove expired port 2024-12-31 biology/ncbi-vdb: Very outdated, unmaintained and unsupported upstream --- MOVED | 1 + biology/Makefile | 1 - biology/ncbi-vdb/Makefile | 69 ------ biology/ncbi-vdb/distinfo | 5 - biology/ncbi-vdb/files/Makefile.bsd | 72 ------ biology/ncbi-vdb/files/patch-build_Makefile.clang | 30 --- biology/ncbi-vdb/files/patch-build_Makefile.env | 28 --- biology/ncbi-vdb/files/patch-build_Makefile.gcc | 35 --- .../ncbi-vdb/files/patch-build_Makefile.install | 11 - biology/ncbi-vdb/files/patch-build_Makefile.shell | 31 --- biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh | 22 -- biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh | 22 -- biology/ncbi-vdb/files/patch-build_ld.sh | 49 ---- biology/ncbi-vdb/files/patch-hdf5 | 30 --- biology/ncbi-vdb/files/patch-libs_Makefile | 12 - biology/ncbi-vdb/files/patch-libs_kfg_config.c | 20 -- .../ncbi-vdb/files/patch-libs_klib_unix_systime.c | 11 - biology/ncbi-vdb/files/patch-libs_kns_Makefile | 13 -- .../ncbi-vdb/files/patch-libs_kns_unix_syssock.c | 10 - .../ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile | 40 ---- biology/ncbi-vdb/files/patch-libs_search_Makefile | 12 - biology/ncbi-vdb/files/patch-setup_konfigure.perl | 253 --------------------- biology/ncbi-vdb/files/patch-setup_os-arch.prl | 20 -- biology/ncbi-vdb/files/patch-setup_package.prl | 26 --- .../ncbi-vdb/files/patch-test_kapp_run-sig-core.sh | 49 ---- biology/ncbi-vdb/files/patch-test_kfg_kfgtest.cpp | 11 - .../ncbi-vdb/files/patch-test_klib_printf-test.c | 11 - biology/ncbi-vdb/files/patch-test_kns_Makefile | 32 --- .../files/patch-test_vdb_test-dependencies.cpp | 11 - ...s_redirect-rejected-names-cgi-http-to-https.cpp | 11 - biology/ncbi-vdb/pkg-descr | 5 - biology/ncbi-vdb/pkg-plist | 32 --- 32 files changed, 1 insertion(+), 984 deletions(-) diff --git a/MOVED b/MOVED index d6a993e3bd05..ae53e7dcd058 100644 --- a/MOVED +++ b/MOVED @@ -3811,3 +3811,4 @@ net-mgmt/zabbix64-server||2025-01-01|Has expired: Zabbix 6.4 is expected to reac www/webtrees20|www/webtrees21|2025-01-01|Has expired: Uses obsolete PHP version; use www/webtrees21 or www/webtrees22 instead dns/py-idna_ssl||2025-01-01|Has expired: Upstream repository has been archived on Oct 22, 2020 science/py-nilearn||2025-01-01|Has expired: Depends on expired devel/py-codecov +biology/ncbi-vdb||2025-01-01|Has expired: Very outdated, unmaintained and unsupported upstream diff --git a/biology/Makefile b/biology/Makefile index 35727e12139c..45b22213c546 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -123,7 +123,6 @@ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit - SUBDIR += ncbi-vdb SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene diff --git a/biology/ncbi-vdb/Makefile b/biology/ncbi-vdb/Makefile deleted file mode 100644 index fc60b954bcd8..000000000000 --- a/biology/ncbi-vdb/Makefile +++ /dev/null @@ -1,69 +0,0 @@ -PORTNAME= ncbi-vdb -DISTVERSION= 2.11.0 -PORTREVISION= 6 -CATEGORIES= biology - -MAINTAINER= ports@FreeBSD.org -COMMENT= NCBI's virtualized back-end for accessing Sequence Read Archive -WWW= https://github.com/ncbi/ncbi-vdb/wiki - -LICENSE= PD -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Very outdated, unmaintained and unsupported upstream -EXPIRATION_DATE=2024-12-31 - -ONLY_FOR_ARCHS= amd64 i386 -ONLY_FOR_ARCHS_REASON= libs/search/nucstrstr.c requires SSE2 instructions - -BUILD_DEPENDS= bash:shells/bash \ - libepoll-shim>0:devel/libepoll-shim - -LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libmbedtls.so:security/mbedtls - -USES= compiler:c11 gmake gnome localbase:ldflags perl5 shebangfix -USE_GNOME= libxml2 -USE_PERL5= build -USE_LDCONFIG= yes - -USE_GITHUB= yes -GH_ACCOUNT= ncbi -GH_TUPLE+= ncbi:ngs:${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 <bsd.port.mk> diff --git a/biology/ncbi-vdb/distinfo b/biology/ncbi-vdb/distinfo deleted file mode 100644 index d5c8684089f1..000000000000 --- a/biology/ncbi-vdb/distinfo +++ /dev/null @@ -1,5 +0,0 @@ -TIMESTAMP = 1618218620 -SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa -SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539 -SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc -SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365 diff --git a/biology/ncbi-vdb/files/Makefile.bsd b/biology/ncbi-vdb/files/Makefile.bsd deleted file mode 100644 index 7692ec277948..000000000000 --- a/biology/ncbi-vdb/files/Makefile.bsd +++ /dev/null @@ -1,72 +0,0 @@ -# =========================================================================== -# -# PUBLIC DOMAIN NOTICE -# National Center for Biotechnology Information -# -# This software/database is a "United States Government Work" under the -# terms of the United States Copyright Act. It was written as part of -# the author's official duties as a United States Government employee and -# thus cannot be copyrighted. This software/database is freely available -# to the public for use. The National Library of Medicine and the U.S. -# Government have not placed any restriction on its use or reproduction. -# -# Although all reasonable efforts have been taken to ensure the accuracy -# and reliability of the software and data, the NLM and the U.S. -# Government do not and cannot warrant the performance or results that -# may be obtained by using this software or data. The NLM and the U.S. -# Government disclaim all warranties, express or implied, including -# warranties of performance, merchantability or fitness for any particular -# purpose. -# -# Please cite the author in any work or product based on this material. -# -# =========================================================================== - - -# default compiler -ifeq (,$(COMP)) - COMP = clang -endif - -# handle attempts to set cross-compilation architecture -# note that if your installation is set up for cross compilation, -# you can try to enable it on your own. -ifeq (i386,$(ARCH)) -i386: - @ true -x86_64: - @ echo "FreeBSD builds do not support cross-compilation to this architecture" -endif - -ifeq (x86_64,$(ARCH)) -i386: - @ echo "FreeBSD builds do not support cross-compilation to this architecture" -x86_64: - @ true -endif - -.PHONY: i386 x86_64 - - -# library prefix -LPFX = lib - -# file extensions -OBJX = o -LOBX = pic.o -LIBX = a -SHLX = so - -# compilation defines -DEFINES := -DBSD -DUNIX -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=bsd$(BITS) - -# FreeBSD is a Unix variant; for most cases, linux sources do well -OS_DAD = linux -OS_GDAD = unix - -# flex+bison: on Mac, use source-controlled generated .c/.h files -YACC = @ true -LEX = @ true - -# build matrix -COMPILERS = CLANG GCC diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.clang b/biology/ncbi-vdb/files/patch-build_Makefile.clang deleted file mode 100644 index fb43d0f3964d..000000000000 --- a/biology/ncbi-vdb/files/patch-build_Makefile.clang +++ /dev/null @@ -1,30 +0,0 @@ ---- build/Makefile.clang.orig 2021-03-15 18:16:43 UTC -+++ build/Makefile.clang -@@ -24,23 +24,23 @@ - - - # compilers --CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \ -+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \ - $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD --CP = @ $(TOP)/build/cc.sh $(OS) 'clang++ -c' \ -+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \ - $(CHECKSUM) --objx $(OBJX) -stdlib=libc++ --cflags "$(CPFLAGS)" -MD - - # C preprocessor - PP = gcc -E $(CFLAGS) - - # linkers --LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang \ -+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ - -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) - - LPFLAGS = $(LDFLAGS) - --LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) clang++ \ -+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ - -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.env b/biology/ncbi-vdb/files/patch-build_Makefile.env deleted file mode 100644 index b6f7158d65d3..000000000000 --- a/biology/ncbi-vdb/files/patch-build_Makefile.env +++ /dev/null @@ -1,28 +0,0 @@ ---- build/Makefile.env.orig 2021-03-15 18:16:43 UTC -+++ build/Makefile.env -@@ -333,6 +333,25 @@ INCDIRS = \ - $(addprefix -I,$(XTINC) $(NGSINC)) \ - -I. - -+# linker paths -+LDPATHS = -+ -+ifneq (,$(HDF5_LIBDIR)) -+ LDPATHS += -L$(HDF5_LIBDIR) -+endif -+ifneq (,$(XML2_LIBDIR)) -+ LDPATHS += -L$(XML2_LIBDIR) -+endif -+ifneq (,$(MAGIC_LIBDIR)) -+ LDPATHS += -L$(MAGIC_LIBDIR) -+endif -+ifneq (,$(MBEDTLS_LIBDIR)) -+ LDPATHS += -L$(MBEDTLS_LIBDIR) -+endif -+ifneq (,$(FUSE_LIBDIR)) -+ LDPATHS += -L$(FUSE_LIBDIR) -+endif -+ - - # defines that describe os & architecture - DLLX ?= $(SHLX) diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.gcc b/biology/ncbi-vdb/files/patch-build_Makefile.gcc deleted file mode 100644 index b7df82ef7c9f..000000000000 --- a/biology/ncbi-vdb/files/patch-build_Makefile.gcc +++ /dev/null @@ -1,35 +0,0 @@ ---- build/Makefile.gcc.orig 2017-07-14 21:55:36 UTC -+++ build/Makefile.gcc -@@ -22,25 +22,27 @@ - # - # =========================================================================== - -+CCNAME ?= gcc -+CXXNAME ?= g++ - - # compilers --CC = @ $(TOP)/build/cc.sh $(OS) 'gcc -c' \ -+CC = @ $(TOP)/build/cc.sh $(OS) '$(CCNAME) -c' \ - $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD --CP = @ $(TOP)/build/cc.sh $(OS) 'g++ -c' \ -+CP = @ $(TOP)/build/cc.sh $(OS) '$(CXXNAME) -c' \ - $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD - - # C preprocessor --PP = gcc -E $(CFLAGS) -+PP = $(CCNAME) -E $(CFLAGS) - - # linkers --LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ -+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CCNAME) \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ - -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) - - LPFLAGS = $(LDFLAGS) - --LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ -+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) $(CXXNAME) \ - --build $(BUILD) --ldflags "$(LPFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ - -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.install b/biology/ncbi-vdb/files/patch-build_Makefile.install deleted file mode 100644 index edd0682cdf14..000000000000 --- a/biology/ncbi-vdb/files/patch-build_Makefile.install +++ /dev/null @@ -1,11 +0,0 @@ ---- build/Makefile.install.orig 2021-03-15 18:16:43 UTC -+++ build/Makefile.install -@@ -69,7 +69,7 @@ ifeq (1,$(HAVE_HDF5)) - endif - - --LIB_TARGET = $(INST_LIBDIR)$(BITS) -+LIB_TARGET = $(INST_LIBDIR) - - LIBRARIES_WITH_PREFIX = \ - $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL)) diff --git a/biology/ncbi-vdb/files/patch-build_Makefile.shell b/biology/ncbi-vdb/files/patch-build_Makefile.shell deleted file mode 100644 index c331ad799a68..000000000000 --- a/biology/ncbi-vdb/files/patch-build_Makefile.shell +++ /dev/null @@ -1,31 +0,0 @@ ---- build/Makefile.shell.orig 2017-07-14 21:55:36 UTC -+++ build/Makefile.shell -@@ -36,6 +36,9 @@ endif - ifeq (Linux, $(UNAME)) - HOST_OS = linux - endif -+ifeq (FreeBSD, $(UNAME)) -+ HOST_OS = bsd -+endif - ifeq (SunOS, $(UNAME)) - HOST_OS = sun - ARCHITECTURES = x86_64 i386 -@@ -83,6 +86,9 @@ else - ifeq (x86_64, $(MARCH)) - HOST_ARCH = x86_64 - endif -+ ifeq (amd64, $(MARCH)) -+ HOST_ARCH = x86_64 -+ endif - ifeq (i86pc, $(MARCH)) - HOST_ARCH = x86_64 - ARCHITECTURES = x86_64 i386 -@@ -93,7 +99,7 @@ else - endif - endif - --ARCH = $(HOST_ARCH) -+override ARCH = $(HOST_ARCH) - REMOTE_ARCH = $(ARCH) - - # pick up dependencies from object directory diff --git a/biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh b/biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh deleted file mode 100644 index 074f7721b564..000000000000 --- a/biology/ncbi-vdb/files/patch-build_ld.bsd.dlib.sh +++ /dev/null @@ -1,22 +0,0 @@ ---- build/ld.bsd.dlib.sh.orig 2017-10-27 07:23:08 UTC -+++ build/ld.bsd.dlib.sh -@@ -51,8 +51,8 @@ case "$LD" in - g*) - source "${0%dlib.sh}gcc.sh" - ;; --i*) -- source "${0%dlib.sh}icc.sh" -+c*) -+ source "${0%dlib.sh}clang.sh" - ;; - *) - echo "$SELF_NAME: unrecognized ld tool - '$LD'" -@@ -100,7 +100,7 @@ then - # always load libdl as shared library - load-ref-symbols - load-dynamic -- CMD="$CMD -ldl" -+# CMD="$CMD -ldl" - ;; - - -l*) diff --git a/biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh b/biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh deleted file mode 100644 index a4ea00c176f1..000000000000 --- a/biology/ncbi-vdb/files/patch-build_ld.bsd.exe.sh +++ /dev/null @@ -1,22 +0,0 @@ ---- build/ld.bsd.exe.sh.orig 2017-10-27 07:23:08 UTC -+++ build/ld.bsd.exe.sh -@@ -51,8 +51,8 @@ case "$LD" in - g*) - source "${0%exe.sh}gcc.sh" - ;; --i*) -- source "${0%exe.sh}icc.sh" -+c*) -+ source "${0%exe.sh}clang.sh" - ;; - *) - echo "$SELF_NAME: unrecognized ld tool - '$LD'" -@@ -108,7 +108,7 @@ then - # always load libdl as shared library - load-ref-symbols - load-dynamic -- CMD="$CMD -ldl" -+# CMD="$CMD -ldl" - ;; - - -l*) diff --git a/biology/ncbi-vdb/files/patch-build_ld.sh b/biology/ncbi-vdb/files/patch-build_ld.sh deleted file mode 100644 index 900d7e566356..000000000000 --- a/biology/ncbi-vdb/files/patch-build_ld.sh +++ /dev/null @@ -1,49 +0,0 @@ ---- build/ld.sh.orig 2021-04-12 06:10:01 UTC -+++ build/ld.sh -@@ -68,6 +68,8 @@ HAVE_M=0 - NEED_M=1 - HAVE_XML=0 - NEED_XML=0 -+HAVE_MBEDTLS=0 -+NEED_MBEDTLS=0 - HAVE_KFC=0 - HAVE_KAPP=0 - HAVE_NCBI_VDB=0 -@@ -297,11 +299,12 @@ do - -[lds]ncbi-vdb) - HAVE_NCBI_VDB=1 - KPROC=4 -- HAVE_GZIP=1 -- HAVE_BZIP=1 -+ NEED_GZIP=1 -+ NEED_BZIP=1 - HAVE_KFC=1 - NEED_M=1 - NEED_XML=1 -+ NEED_MBEDTLS=1 - LIBS="$LIBS $1" - ;; - -[lds]ncbi-ngs-c++) -@@ -310,11 +313,12 @@ do - -[lds]ncbi-wvdb) - HAVE_NCBI_WVDB=1 - KPROC=4 -- HAVE_GZIP=1 -- HAVE_BZIP=1 -+ NEED_GZIP=1 -+ NEED_BZIP=1 - HAVE_KFC=1 - NEED_M=16 - NEED_XML=1 -+ NEED_MBEDTLS=1 - LIBS="$LIBS $1" - ;; - -@@ -505,6 +509,7 @@ fi - # supply missing libraries - [ $HAVE_GZIP -eq 0 ] && [ $NEED_GZIP -ne 0 ] && LIBS="$LIBS -lz" - [ $HAVE_BZIP -eq 0 ] && [ $NEED_BZIP -ne 0 ] && LIBS="$LIBS -lbz2" -+[ $HAVE_MBEDTLS -eq 0 ] && [ $NEED_MBEDTLS -ne 0 ] && LIBS="$LIBS -lmbedtls -lmbedcrypto -lmbedx509" - [ $HAVE_DL -eq 0 ] && [ $NEED_DL -ne 0 ] && LIBS="$LIBS -ldl" - [ $HAVE_M -eq 0 ] && [ $NEED_M -ne 0 ] && HAVE_M=16 - [ $HAVE_XML -eq 0 ] && [ $NEED_XML -ne 0 ] && HAVE_XML=32 diff --git a/biology/ncbi-vdb/files/patch-hdf5 b/biology/ncbi-vdb/files/patch-hdf5 deleted file mode 100644 index 0566ee28dc25..000000000000 --- a/biology/ncbi-vdb/files/patch-hdf5 +++ /dev/null @@ -1,30 +0,0 @@ ---- interfaces/ext/hdf5/H5Opublic.h.orig 2021-03-15 18:16:43 UTC -+++ interfaces/ext/hdf5/H5Opublic.h -@@ -150,8 +150,13 @@ H5_DLL hid_t H5Oopen_by_idx(hid_t loc_id, const char * - H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t lapl_id); - H5_DLL htri_t H5Oexists_by_name(hid_t loc_id, const char *name, hid_t lapl_id); - H5_DLL herr_t H5Oget_info(hid_t loc_id, H5O_info_t *oinfo); -+#if H5_VERSION_GE(1,12,0) -+H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo, unsigned fields, -+ hid_t lapl_id); -+#else - H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo, - hid_t lapl_id); -+#endif - H5_DLL herr_t H5Oget_info_by_idx(hid_t loc_id, const char *group_name, - H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5O_info_t *oinfo, - hid_t lapl_id); ---- libs/hdf5/hdf5dir.c.orig 2021-03-15 18:16:43 UTC -+++ libs/hdf5/hdf5dir.c -@@ -292,7 +292,11 @@ rc_t CC HDF5DirVisitUpdate ( HDF5Dir *self, bool recur - static uint32_t HDF5DirPathTypeOnBuffer( const HDF5Dir *self, const char *buffer ) - { - H5O_info_t obj_info; -+#if H5_VERSION_GE(1,12,0) -+ herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5O_INFO_BASIC, H5P_DEFAULT ); -+#else - herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5P_DEFAULT ); -+#endif - if ( h5e >= 0 ) - { - switch( obj_info.type ) diff --git a/biology/ncbi-vdb/files/patch-libs_Makefile b/biology/ncbi-vdb/files/patch-libs_Makefile deleted file mode 100644 index f444241b68f9..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_Makefile +++ /dev/null @@ -1,12 +0,0 @@ -To omit building bundled libraries. - ---- libs/Makefile.orig 2021-03-15 18:16:43 UTC -+++ libs/Makefile -@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config - # default - # - MAIN_SUBDIRS = \ -- ext \ - kfc \ - klib \ - kproc \ diff --git a/biology/ncbi-vdb/files/patch-libs_kfg_config.c b/biology/ncbi-vdb/files/patch-libs_kfg_config.c deleted file mode 100644 index d82d3e9143ed..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_kfg_config.c +++ /dev/null @@ -1,20 +0,0 @@ ---- libs/kfg/config.c.orig 2021-03-15 18:16:43 UTC -+++ libs/kfg/config.c -@@ -2577,7 +2577,7 @@ bool load_from_std_location ( KConfig *self, const KDi - const char * std_locs [] = - { - #if ! WINDOWS -- "/etc/ncbi", -+ @@PREFIX@@ "/etc/ncbi", - #else - "/c/ncbi", - #endif -@@ -2850,6 +2850,8 @@ void add_predefined_nodes ( KConfig * self, const char - #define OS "win" - #elif SUN - #define OS "sun" -+#elif BSD -+ #define OS "bsd" - #else - #error unrecognized OS - #endif diff --git a/biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c b/biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c deleted file mode 100644 index 781fd4b75403..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_klib_unix_systime.c +++ /dev/null @@ -1,11 +0,0 @@ ---- libs/klib/unix/systime.c.orig 2017-07-14 21:55:36 UTC -+++ libs/klib/unix/systime.c -@@ -142,7 +142,7 @@ LIB_EXPORT KTime_t CC KTimeMakeTime ( co - t . tm_isdst = self -> dst; - - ts = mktime ( &t ); -- ts -= timezone; -+ ts += localtime(&ts)->tm_gmtoff; - } - - return ts; diff --git a/biology/ncbi-vdb/files/patch-libs_kns_Makefile b/biology/ncbi-vdb/files/patch-libs_kns_Makefile deleted file mode 100644 index 6438e3f6bfa6..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_kns_Makefile +++ /dev/null @@ -1,13 +0,0 @@ ---- libs/kns/Makefile.orig 2017-07-14 21:55:36 UTC -+++ libs/kns/Makefile -@@ -39,6 +39,10 @@ OBJFILES = \ - - include $(TOP)/build/Makefile.env - -+ifdef MBEDTLS_INCDIR -+ INCDIRS += $(addprefix -I,$(MBEDTLS_INCDIR)) -+endif -+ - RWORKDIR = $(TOP)/$(MODULE) - - #------------------------------------------------------------------------------- diff --git a/biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c b/biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c deleted file mode 100644 index a188b1c12539..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_kns_unix_syssock.c +++ /dev/null @@ -1,10 +0,0 @@ ---- libs/kns/unix/syssock.c.orig 2017-07-14 21:55:36 UTC -+++ libs/kns/unix/syssock.c -@@ -66,6 +66,7 @@ - #include <sys/types.h> - #include <sys/socket.h> - #include <sys/un.h> -+#include <netinet/in.h> - #include <netinet/tcp.h> - #include <poll.h> - #include <unistd.h> diff --git a/biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile b/biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile deleted file mode 100644 index 724f06235fcd..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_ncbi-vdb_Makefile +++ /dev/null @@ -1,40 +0,0 @@ ---- libs/ncbi-vdb/Makefile.orig 2021-03-15 18:16:43 UTC -+++ libs/ncbi-vdb/Makefile -@@ -121,15 +121,16 @@ LDFLAGS += -L$(XML2_LIBDIR) - endif - endif - -+ifneq (,$(MBEDTLS_LIBDIR)) -+LDFLAGS += -L$(MBEDTLS_LIBDIR) -+endif -+ - VDB_LIB_CMN = \ - align-access \ - ncbi-bam \ - vfs \ - cloud \ - $(LIBKXML) \ -- mbedx509 \ -- mbedtls \ -- mbedcrypto \ - kns \ - kfg \ - krypto \ -@@ -138,9 +139,7 @@ VDB_LIB_CMN = \ - klib \ - kproc \ - $(LIBKQ) \ -- kfc \ -- bz2 \ -- z \ -+ kfc - - VDB_LIB_RD = \ - align-reader \ -@@ -198,4 +197,4 @@ fuzz: - $(TOP)/build/ld.sh linux x86_64 gcc --build dbg --ldflags "-g -m64" --objx o --shlx so --libx a --srcdir $(SRCDIR) --bindir $(BINDIR) --slib -o $(FLIBDIR)/libncbi-vdb.$(LIBX) -L$(FLIBDIR) $(VDB_LIB) $(VDB_NGS_LIB) - - cleanfuzz: -- rm -rf $(FLIBDIR)/* -\ No newline at end of file -+ rm -rf $(FLIBDIR)/* diff --git a/biology/ncbi-vdb/files/patch-libs_search_Makefile b/biology/ncbi-vdb/files/patch-libs_search_Makefile deleted file mode 100644 index 3c01af3268be..000000000000 --- a/biology/ncbi-vdb/files/patch-libs_search_Makefile +++ /dev/null @@ -1,12 +0,0 @@ ---- libs/search/Makefile.orig 2017-07-14 21:55:36 UTC -+++ libs/search/Makefile -@@ -39,6 +39,9 @@ OBJFILES = \ - - include $(TOP)/build/Makefile.env - -+CARCH += -msse2 -+# nucstrstr.c requires SSE2 -+ - #------------------------------------------------------------------------------- - # outer targets - # diff --git a/biology/ncbi-vdb/files/patch-setup_konfigure.perl b/biology/ncbi-vdb/files/patch-setup_konfigure.perl deleted file mode 100644 index 39a2926d5511..000000000000 --- a/biology/ncbi-vdb/files/patch-setup_konfigure.perl +++ /dev/null @@ -1,253 +0,0 @@ ---- setup/konfigure.perl.orig 2021-03-15 18:16:43 UTC -+++ setup/konfigure.perl -@@ -192,7 +192,7 @@ if ($OPT{'help'}) { - foreach (@ARGV) { - @_ = split('='); - next if ($#_ != 1); -- $OPT{$_[0]} = $_[1] if ($_[0] eq 'CXX' || $_[0] eq 'LDFLAGS'); -+ $OPT{$_[0]} = $_[1] if ($_[0] eq 'CC' || $_[0] eq 'CXX' || $_[0] eq 'LDFLAGS' || $_[0] eq 'TOOLS'); - } - - println "Configuring $PACKAGE_NAME package"; -@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN); - my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch(); - println $OSTYPE unless ($AUTORUN); - --unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { -+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { - println "configure: error: unsupported system '$OSTYPE'"; - exit 1; - } -@@ -225,7 +225,7 @@ if ($OS eq 'linux') { - - print "checking machine architecture... " unless ($AUTORUN); - println $MARCH unless ($AUTORUN); --unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { -+unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { - println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'"; - exit 1; - } -@@ -310,7 +310,7 @@ print "checking for supported architecture... " unless - - my $BITS; - --if ($MARCH =~ /x86_64/i) { -+if ($MARCH =~ /(x86_|amd)64/i) { - $BITS = 64; - } elsif ($MARCH eq 'fat86') { - $BITS = '32_64'; -@@ -337,6 +337,19 @@ if ($OSTYPE =~ /linux/i) { - $OSINC = 'unix'; - $TOOLS = 'gcc' unless ($TOOLS); - $PYTHON = 'python'; -+} elsif ($OSTYPE =~ /freebsd/i) { -+ $LPFX = 'lib'; -+ $OBJX = 'o'; -+ $LOBX = 'pic.o'; -+ $LIBX = 'a'; -+ $SHLX = 'so'; -+ $EXEX = ''; -+ $OSINC = 'unix'; -+ unless ($TOOLS) { -+ $TOOLS = 'clang'; -+ $TOOLS = $OPT{TOOLS} if ($OPT{TOOLS}); -+ } -+ $PYTHON = $ENV{FREEBSD_PYTHON_CMD}; - } elsif ($OSTYPE =~ /darwin/i) { - $LPFX = 'lib'; - $OBJX = 'o'; -@@ -362,17 +375,19 @@ my ($ARCH_FL, $DBG, $OPT, $PIC, $INC, $MD, $LDFLAGS) = - - print "checking for supported tool chain... " unless ($AUTORUN); - -+$CC = $OPT{CC } if ($OPT{CC }); - $CPP = $OPT{CXX } if ($OPT{CXX }); - $LDFLAGS = $OPT{LDFLAGS} if ($OPT{LDFLAGS}); - - if ($TOOLS =~ /gcc$/) { - $CPP = 'g++' unless ($CPP); -- $CC = "$TOOLS -c"; -+ $CC = 'gcc' unless ($CC); -+ $LD = $CC; -+ $CC = "$CC -c"; - $CP = "$CPP -c"; - $AR = 'ar rc'; - $ARX = 'ar x'; - $ARLS = 'ar t'; -- $LD = $TOOLS; - $LP = $CPP; - - $DBG = '-g -DDEBUG'; -@@ -382,21 +397,24 @@ if ($TOOLS =~ /gcc$/) { - $MD = '-MD'; - } elsif ($TOOLS eq 'clang') { - $CPP = 'clang++' unless ($CPP); -- $CC = 'clang -c'; -- my $versionMin = '-mmacosx-version-min=10.10'; -+ $CC = 'clang' unless ($CC); -+ $LD = $CC; -+ $CC = "$CC -c"; -+ my $versionMin = ''; -+ $versionMin = '-mmacosx-version-min=10.6' if ($OSTYPE =~ /darwin/i); - $CP = "$CPP -c $versionMin"; - if ($BITS ne '32_64') { - $ARCH_FL = '-arch i386' if ($BITS == 32); - $OPT = '-O3'; - $AR = 'ar rc'; -- $LD = "clang $ARCH_FL"; -+ $LD = "$LD $ARCH_FL"; - $LP = "$CPP $versionMin $ARCH_FL"; - } else { - $MAKE_MANIFEST = '( echo "$^" > $@/manifest )'; - $ARCH_FL = '-arch i386 -arch x86_64'; - $OPT = '-O3'; - $AR = 'libtool -static -o'; -- $LD = "clang -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; -+ $LD = "$LD -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; - $LP = "$CPP $versionMin -Wl,-arch_multiple $ARCH_FL -Wl,-all_load"; - } - $ARX = 'ar x'; -@@ -826,13 +844,13 @@ OS_ARCH = \$(shell perl \$(TOP)/setup/os-arch.perl) - # install paths - EndText - -- L($F, "INST_BINDIR = $OPT{'bindir'}" ) if ($OPT{'bindir'}); -- L($F, "INST_LIBDIR = $OPT{'libdir'}" ) if ($OPT{'libdir'}); -- L($F, "INST_INCDIR = $OPT{'includedir'}" ) if ($OPT{'includedir'}); -- L($F, "INST_SCHEMADIR = $OPT{'shemadir'}" ) if ($OPT{'shemadir'}); -- L($F, "INST_SHAREDIR = $OPT{'sharedir'}" ) if ($OPT{'sharedir'}); -- L($F, "INST_JARDIR = $OPT{'javadir'}" ) if ($OPT{'javadir'}); -- L($F, "INST_PYTHONDIR = $OPT{'pythondir'}") if ($OPT{'pythondir'}); -+ L($F, "INST_BINDIR = \$(DESTDIR)$OPT{'bindir'}" ) if ($OPT{'bindir'}); -+ L($F, "INST_LIBDIR = \$(DESTDIR)$OPT{'libdir'}" ) if ($OPT{'libdir'}); -+ L($F, "INST_INCDIR = \$(DESTDIR)$OPT{'includedir'}" ) if ($OPT{'includedir'}); -+ L($F, "INST_SCHEMADIR = \$(DESTDIR)$OPT{'shemadir'}" ) if ($OPT{'shemadir'}); -+ L($F, "INST_SHAREDIR = \$(DESTDIR)$OPT{'sharedir'}" ) if ($OPT{'sharedir'}); -+ L($F, "INST_JARDIR = \$(DESTDIR)$OPT{'javadir'}" ) if ($OPT{'javadir'}); -+ L($F, "INST_PYTHONDIR = \$(DESTDIR)$OPT{'pythondir'}") if ($OPT{'pythondir'}); - - my ($E_VERSION_SHLX, $VERSION_SHLX, - $E_MAJVERS_SHLX , $MAJMIN_SHLX, $MAJVERS_SHLX); -@@ -896,7 +914,7 @@ MAJMIN_EXEX = \$(EXEX).\$(MAJMIN) - MAJVERS_EXEX = \$(EXEX).\$(MAJVERS) - - # system architecture and wordsize --ARCH = $ARCH -+override ARCH = $ARCH - EndText - - L($F, "# ARCH = $ARCH ( $MARCH )") if ($ARCH ne $MARCH); -@@ -932,7 +950,7 @@ EndText - } - L($F, "PIC = $PIC") if ($PIC); - if ($PKG{LNG} eq 'C') { -- if ($TOOLS =~ /clang/i) { -+ if ($OSTYPE =~ /darwin/i) { - L($F, 'SONAME = -install_name ' . - '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); - L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\'); -@@ -1043,7 +1061,7 @@ EndText - L($F, '# directory rules'); - if ($PKG{LNG} eq 'C') { - L($F, '$(BINDIR) $(LIBDIR) $(ILIBDIR) ' -- . '$(OBJDIR) $(INST_LIBDIR) $(INST_LIBDIR)$(BITS):'); -+ . '$(OBJDIR) $(INST_LIBDIR):'); - T($F, 'mkdir -p $@'); - } elsif ($PKG{LNG} eq 'JAVA') { - # test if we have jni header path -@@ -1073,12 +1091,12 @@ EndText - L($F, 'export CONFIGURE_FOUND_XML2'); - L($F); - -- if ($OS eq 'linux' || $OS eq 'mac') { -+ if ($OS eq 'linux' || $OS eq 'bsd' || $OS eq 'mac') { - L($F, '# installation rules'); - L($F, -- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)'); -+ '$(INST_LIBDIR)/%.$(VERSION_LIBX): $(LIBDIR)/%.$(VERSION_LIBX)'); - T($F, '@ echo -n "installing \'$(@F)\'... "'); -- T($F, '@ if cp $^ $@ && chmod 644 $@; \\'); -+ T($F, '@ if $(BSD_INSTALL_DATA) $^ $@; \\'); - T($F, ' then \\'); - T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' - . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@) ' -@@ -1087,7 +1105,7 @@ EndText - T($F, ' ln -s $(patsubst %$(VERSION),%$(MAJVERS),$(@F)) ' - . '$(patsubst %$(VERSION_LIBX),%$(LIBX),$@); \\'); - T($F, ' ln -s $(patsubst %$(VERSION_LIBX),%$(LIBX),$(@F)) ' . -- '$(INST_LIBDIR)$(BITS)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));' -+ '$(INST_LIBDIR)/$(patsubst %.$(VERSION_LIBX),%-static.$(LIBX),$(@F));' - . ' \\'); - T($F, ' echo success; \\'); - T($F, ' else \\'); -@@ -1097,15 +1115,15 @@ EndText - L($F); - - L($F, -- '$(INST_LIBDIR)$(BITS)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)'); -+ '$(INST_LIBDIR)/%.$(VERSION_SHLX): $(LIBDIR)/%.$(VERSION_SHLX)'); - T($F, '@ echo -n "installing \'$(@F)\'... "'); -- T($F, '@ if cp $^ $@ && chmod 755 $@; \\'); -+ T($F, '@ if $(BSD_INSTALL_LIB) $^ $@; \\'); - T($F, ' then \\'); - if ($OS ne 'mac') { - T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' - . '$(patsubst %$(VERSION_SHLX),%$(SHLX),$@); \\'); - } -- if ($OS eq 'linux') { -+ if ($OS eq 'linux' || $OS eq 'bsd') { - T($F, ' ln -s $(@F) $(patsubst %$(VERSION),%$(MAJVERS),$@); \\'); - } elsif ($OS eq 'mac') { - T($F, ' ln -sf $(@F) ' -@@ -1124,7 +1142,7 @@ EndText - - L($F, '$(INST_BINDIR)/%$(VERSION_EXEX): $(BINDIR)/%$(VERSION_EXEX)'); - T($F, '@ echo -n "installing \'$(@F)\'... "'); -- T($F, '@ if cp $^ $@ && chmod 755 $@; \\'); -+ T($F, '@ if $(BSD_INSTALL_PROGRAM) $^ $@; \\'); - T($F, ' then \\'); - T($F, ' rm -f $(patsubst %$(VERSION),%$(MAJVERS),$@) ' - . '$(patsubst %$(VERSION_EXEX),%$(EXEX),$@); \\'); -@@ -1406,7 +1424,7 @@ sub find_in_dir { - ++$found; - } - if (! $found) { -- my $libdir = File::Spec->catdir($dir, 'lib' . $BITS); -+ my $libdir = File::Spec->catdir($dir, 'lib'); - my $f = File::Spec->catdir($libdir, $lib); - print "\tchecking $f\n\t" if ($OPT{'debug'}); - if (-e $f) { -@@ -1628,12 +1646,12 @@ sub find_lib { - - sub check_compiler { - my ($t, $n, $I, @l) = @_; -- my $tool = $TOOLS; -+ my $tool = $CC; - - if ($t eq 'L') { - print "checking for $n library... "; - } elsif ($t eq 'O') { -- if ($tool && ($tool =~ /gcc$/ || $tool =~ /g\+\+$/)) { -+ if ($tool && ($tool =~ /gcc/ || $tool =~ /g\+\+/)) { - print "checking whether $tool accepts $n... "; - } else { - return; -@@ -1663,6 +1681,9 @@ sub check_compiler { - } elsif ($n eq 'magic') { - $library = '-lmagic'; - $log = '#include <magic.h> \n int main() { magic_open (0); }\n' -+ } elsif ($n eq 'mbedtls') { -+ $library = '-lmbedtls'; -+ $log = '#include <mbedtls/version.h> \n int main() { mbedtls_version_get_string(0); }\n' - } elsif ($n eq 'xml2') { - $library = '-lxml2'; - $library .= ' -liconv' if ($OS eq 'mac'); -@@ -1706,7 +1727,7 @@ sub check_compiler { - } - } - my $gcc = "| $tool -xc $flags " . ($I ? "-I$I " : ' ') -- . ($l ? "-L$l " : ' ') . "- $library"; -+ . ($l ? "-L$l " : ' ') . "-o a.out - $library"; - $gcc .= ' 2> /dev/null' unless ($OPT{'debug'}); - - open GCC, $gcc or last; diff --git a/biology/ncbi-vdb/files/patch-setup_os-arch.prl b/biology/ncbi-vdb/files/patch-setup_os-arch.prl deleted file mode 100644 index 28d9b469c744..000000000000 --- a/biology/ncbi-vdb/files/patch-setup_os-arch.prl +++ /dev/null @@ -1,20 +0,0 @@ ---- setup/os-arch.prl.orig 2021-03-15 18:16:43 UTC -+++ setup/os-arch.prl -@@ -11,6 +11,8 @@ sub OsArch { - chomp $UNAME; - if ($UNAME =~ /Darwin/) { - $HOST_OS = 'mac'; -+ } elsif ($UNAME =~ /.*BSD/) { -+ $HOST_OS = 'bsd'; - } elsif ($UNAME =~ /Linux/) { - $HOST_OS = 'linux'; - } elsif ($UNAME =~ /SunOS/) { -@@ -48,6 +50,8 @@ sub OsArch { - $HOST_ARCH = 'i386'; - } - } elsif ($MARCH =~ /x86_64/) { -+ $HOST_ARCH = 'x86_64'; *** 246 LINES SKIPPED ***
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202501011100.501B0CD6023436>