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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>

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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    2024-12-31 biology/ncbi-vdb: Very outdated, unmaintained and unsupported upstream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 ***



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