Merge lp:~noskcaj/ubuntu/trusty/sra-sdk/ftbfs into lp:ubuntu/trusty/sra-sdk

[Jackson Doak]

New upstream bugfix release (fixes ftbfs)

[Martin Pitt (pitti)]

This was already uploaded as https://launchpad.net/ubuntu/+source/sra-sdk/2.3.3-4~dfsg-1ubuntu1. Note that it still FTBFS on i386.

=== added file '.pc/.quilt_patches'
--- .pc/.quilt_patches	1970-01-01 00:00:00 +0000
+++ .pc/.quilt_patches	2014-04-08 01:47:44 +0000
@@ -0,0 +1,1 @@
+debian/patches
 
=== added file '.pc/.quilt_series'
--- .pc/.quilt_series	1970-01-01 00:00:00 +0000
+++ .pc/.quilt_series	2014-04-08 01:47:44 +0000
@@ -0,0 +1,1 @@
+series
 
=== modified file '.pc/10_portability.patch/build/Makefile.gcc'
--- .pc/10_portability.patch/build/Makefile.gcc	2012-01-10 09:06:14 +0000
+++ .pc/10_portability.patch/build/Makefile.gcc	2014-04-08 01:47:44 +0000
@@ -44,7 +44,14 @@
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
 
 # tool options
-WARN = -Wall # -Wconversion
+WARN = -Wall -Wno-long-long 
+ifneq (sun,$(OS))
+    WARN += -Wno-variadic-macros
+endif
+
+ifeq (linux,$(OS))
+    NO_ARRAY_BOUNDS_WARNING = -Wno-array-bounds
+endif
 
 ifeq (64,$(BITS))
 	CARCH = -m64
@@ -60,12 +67,15 @@
 	DBG = -g
 	OPT = $(WARN)
 	NOPT = $(WARN)
-	PED = -std=c99 -ansi -pedantic
+	# GCC seems unable to use c99 without ansi, which
+	# basically clobbers features back to c89. the options
+	# must be specified in the order shown.
+	PED = -std=c99 -ansi -pedantic # -fdiagnostics-show-option
 else
 
 ifeq (x86_64, $(ARCH))
-	OPT = -O3 -fno-strict-aliasing
+	OPT = -O3 -Wall -Wno-variadic-macros -fno-strict-aliasing
 else
-	OPT = -O3 -fno-strict-aliasing
+	OPT = -O3 -Wno-variadic-macros -fno-strict-aliasing
 endif
 endif
 
=== modified file '.pc/10_portability.patch/build/Makefile.shell'
--- .pc/10_portability.patch/build/Makefile.shell	2012-01-10 09:06:14 +0000
+++ .pc/10_portability.patch/build/Makefile.shell	2014-04-08 01:47:44 +0000
@@ -27,80 +27,124 @@
 UNAME = $(shell uname -s)
 
 ifeq (Darwin, $(UNAME))
-	OS = mac
+	HOST_OS = mac
 endif
 ifeq (Linux, $(UNAME))
-	OS = linux
+	HOST_OS = linux
 endif
 ifeq (SunOS, $(UNAME))
-	OS = sun
+	HOST_OS = sun
+	ARCHITECTURES = x86_64 i386
 endif
 ifeq (xCYGWIN, $(findstring xCYGWIN,x$(UNAME)))
-	OS = win
+	HOST_OS = win
 endif
 ifeq (xMINGW, $(findstring xMINGW,x$(UNAME)))
-	OS = win
+	HOST_OS = win
 endif
 
-# OS flavor is normally OS
-OSFLAV = $(OS)
+# assume build OS is the same as host OS
+OS = $(HOST_OS)
+BUILD_OS = $(OS)
 
 # determine ARCH
-ifeq (mac,$(OS))
-	ARCH = $(shell $(TOP)/build/mac.arch.sh)
+ARCHITECTURES = default
+ifeq (mac,$(HOST_OS))
+	HOST_ARCH = $(shell $(TOP)/build/mac.arch.sh)
 else
 	MARCH = $(shell uname -m)
 
 	ifeq (i386, $(MARCH))
-		ARCH = i386
+		HOST_ARCH = i386
 	endif
 	ifeq (i486, $(MARCH))
-		ARCH = i386
+		HOST_ARCH = i386
 	endif
 	ifeq (i586, $(MARCH))
-		ARCH = i386
+		HOST_ARCH = i386
 	endif
 	ifeq (i686, $(MARCH))
-		ARCH = i386
+		ifeq (WOW64x, $(findstring WOW64x,$(UNAME)x))
+			# 64-bit capable Cygwin. Analyze the version of cl to set the corect architecture
+			CL = $(shell cl.exe 2>&1 >/dev/null)
+			ifeq (for x64, $(findstring for x64, $(CL)))
+				HOST_ARCH = x86_64
+			else
+				HOST_ARCH = i386
+			endif			
+		else
+			HOST_ARCH = i386
+		endif	
 	endif
 	ifeq (x86_64, $(MARCH))
-		ARCH = x86_64
-	endif
-	ifeq (sun4u,$(MARCH))
-		ARCH = sparc32
+		HOST_ARCH = x86_64
+	endif
+	ifeq (i86pc, $(MARCH))
+		HOST_ARCH = x86_64
+		ARCHITECTURES = x86_64 i386
+	endif
+	ifeq (sun4v,$(MARCH))
+		HOST_ARCH = sparc64
+		ARCHITECTURES = sparc64 sparc32
 	endif
 endif
 
-# determine BITS
-ifeq (x86_64, $(ARCH))
-	BITS = 64
+ARCH = $(HOST_ARCH)
+REMOTE_ARCH = $(ARCH)
+
+# pick up dependencies from object directory
+ifdef SRCDIR
+	include $(wildcard *.d)
 else
-	BITS = 32
-endif
-
-# first pass through defines SRCDIR
-ifndef SRCDIR
-
-# set SRCDIR from MODULE
+
+# determine SRCDIR
 ifdef MODULE
 	SRCDIR=$(TOP)/$(MODULE)
 else
 	SRCDIR=$(TOP)
 endif
 
+# set COMP, LNKG and BUILD
+COMP = $(shell test -f $(TOP)/build/COMP && mv $(TOP)/build/COMP $(TOP)/build/COMP.$(OS); test -f $(TOP)/build/COMP.$(OS) && cat $(TOP)/build/COMP.$(OS) || echo gcc)
+LNKG = $(shell test -f $(TOP)/build/STATIC && mv $(TOP)/build/STATIC $(TOP)/build/LNKG.$(OS) && echo stat > $(TOP)/build/LNKG.$(OS); test -f $(TOP)/build/LNKG.$(OS) && cat $(TOP)/build/LNKG.$(OS) || echo stat)
+BUILD = $(shell test -f $(TOP)/build/BUILD && mv $(TOP)/build/BUILD $(TOP)/build/BUILD.$(OS); test -f $(TOP)/build/BUILD.$(OS) && cat $(TOP)/build/BUILD.$(OS) || echo dbg)
+TOOLSET := $(COMP)
+
+ifdef USE_GCC_IF_ICC
+ifeq (icc,$(COMP))
+COMP = gcc
+endif
+ifeq (clang,$(COMP))
+COMP = gcc
+endif
+endif
+
+endif
+
 # set OUTDIR
 ifndef OUTDIR
-	OUTDIR = $(shell test -f $(TOP)/build/OUTDIR.$(OS) && cat $(TOP)/build/OUTDIR.$(OS) || echo $(TOP))
+	OUTDIR = $(shell test -f $(TOP)/build/OUTDIR && mv $(TOP)/build/OUTDIR $(TOP)/build/OUTDIR.$(BUILD_OS); test -f $(TOP)/build/OUTDIR.$(BUILD_OS) && cat $(TOP)/build/OUTDIR.$(BUILD_OS) || echo $(TOP))
 	ifeq (,$(OUTDIR))
 		OUTDIR = $(TOP)
 	endif
-	ifeq (.,$(OUTDIR))
-		OUTDIR = $(TOP)
-	endif
-endif
-
-# set COMP and BUILD
-COMP = $(shell test -f $(TOP)/build/COMP.$(OS) && cat $(TOP)/build/COMP.$(OS) || echo gcc)
-BUILD = $(shell test -f $(TOP)/build/BUILD.$(OS) && cat $(TOP)/build/BUILD.$(OS) || echo dbg)
-
+endif
+ifeq (,$(ROUTDIR))
+	ROUTDIR = $(RHOME)
+endif
+
+# OS flavor is normally OS
+OSFLAV = $(OS)
+
+# determine BITS
+ifeq (x86_64, $(ARCH))
+	BITS = 64
+endif
+ifeq (sparc64, $(ARCH))
+	BITS = 64
+endif
+ifeq (i386, $(ARCH))
+	BITS = 32
+endif
+ifeq (sparc32, $(ARCH))
+	BITS = 32
 endif
 
=== modified file '.pc/applied-patches'
--- .pc/applied-patches	2012-01-10 09:06:14 +0000
+++ .pc/applied-patches	2014-04-08 01:47:44 +0000
@@ -1,1 +1,5 @@
+do_not_build_external_libs.patch
 10_portability.patch
+build-with-system-libbz2-libz.patch
+hardening.patch
+hardening-format-security.patch
 
=== added directory '.pc/build-with-system-libbz2-libz.patch'
=== added directory '.pc/build-with-system-libbz2-libz.patch/libs'
=== added directory '.pc/build-with-system-libbz2-libz.patch/libs/ncbi-vdb'
=== added file '.pc/build-with-system-libbz2-libz.patch/libs/ncbi-vdb/Makefile'
--- .pc/build-with-system-libbz2-libz.patch/libs/ncbi-vdb/Makefile	1970-01-01 00:00:00 +0000
+++ .pc/build-with-system-libbz2-libz.patch/libs/ncbi-vdb/Makefile	2014-04-08 01:47:44 +0000
@@ -0,0 +1,154 @@
+# ===========================================================================
+#
+#                            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: std
+
+TOP ?= $(shell ../../build/abspath.sh ../..)
+MODULE = libs/ncbi-vdb
+
+EXT_LIBS = \
+	libncbi-vdb \
+	libncbi-wvdb
+
+ALL_LIBS = \
+	$(EXT_LIBS)
+
+include $(TOP)/build/Makefile.env
+
+#-------------------------------------------------------------------------------
+# outer targets
+#
+all std: makedirs
+	@ $(MAKE_CMD) $(TARGDIR)/std
+
+$(EXT_LIBS): makedirs
+	@ $(MAKE_CMD) $(LIBDIR)/$@
+
+.PHONY: all std $(ALL_LIBS)
+
+#-------------------------------------------------------------------------------
+# std
+#
+$(TARGDIR)/std: \
+	$(addprefix $(LIBDIR)/,$(EXT_LIBS))
+
+.PHONY: $(TARGDIR)/all $(TARGDIR)/std
+
+#-------------------------------------------------------------------------------
+# clean
+#
+clean: stdclean
+
+.PHONY: clean
+
+#-------------------------------------------------------------------------------
+# virtual db library
+#
+$(LIBDIR)/libncbi-vdb: $(addprefix $(LIBDIR)/libncbi-vdb.,$(LIBEXT))
+
+ifeq (linux,$(OS))
+LIBKFF = kff magic
+LIBVDB_BLAST = vdb-blast
+else
+LIBKFF =
+LIBVDB_BLAST =
+endif
+
+ifeq (win,$(OS))
+LIBENTREZ =
+LIBKQ =
+LIBKXML =
+else
+LIBENTREZ =
+LIBKQ = kq
+LIBKXML = kxml kxfs
+endif
+
+VDB_LIB_CMN = \
+	align-access \
+	bz2 \
+	kfg \
+	kfs \
+	klib \
+	kproc \
+	$(LIBKQ) \
+	krypto \
+	ksrch \
+	$(LIBKXML) \
+	kurl \
+	vfs \
+	z
+
+VDB_LIB_RD = \
+	$(VDB_LIB_CMN) \
+	align-reader \
+	ascp \
+	$(EXT_SCHEMA_MODULES) \
+	kdb \
+	sradb \
+	srareader \
+	$(LIBVDB-BLAST) \
+	vdb
+
+VDB_OBJ = \
+	$(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))
+
+VDB_LIB = \
+	$(addprefix -s,$(VDB_LIB_RD))
+
+$(LIBDIR)/libncbi-vdb.$(SHLX): $(VDB_OBJ)
+	$(LD) --dlib --vers $(SRCDIR) -o $@ $(VDB_LIB)
+
+$(LIBDIR)/libncbi-vdb.$(LIBX): $(VDB_OBJ)
+	$(LD) --slib --vers $(SRCDIR) -o $@ $(VDB_LIB)
+
+#-------------------------------------------------------------------------------
+# update version
+#
+$(LIBDIR)/libncbi-wvdb: $(addprefix $(LIBDIR)/libncbi-wvdb.,$(LIBEXT))
+
+VDB_LIB_RDWR = \
+	$(VDB_LIB_CMN) \
+	align-writer \
+	waxf \
+	wkdb \
+	wsradb \
+	wsraxf \
+	wvdb \
+	$(LIBENTREZ) \
+	wvxf \
+	wwgsxf
+
+WVDB_OBJ = \
+	$(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RDWR)))
+
+WVDB_LIB = \
+	$(addprefix -s,$(VDB_LIB_RDWR))
+
+$(LIBDIR)/libncbi-wvdb.$(SHLX): $(WVDB_OBJ)
+	$(LD) --dlib --vers $(SRCDIR) -o $@ $(WVDB_LIB) -lxml2
+
+$(LIBDIR)/libncbi-wvdb.$(LIBX): $(WVDB_OBJ)
+	$(LD) --slib --vers $(SRCDIR) -o $@ $(WVDB_LIB)
 
=== added directory '.pc/do_not_build_external_libs.patch'
=== added directory '.pc/do_not_build_external_libs.patch/libs'
=== added file '.pc/do_not_build_external_libs.patch/libs/Makefile'
--- .pc/do_not_build_external_libs.patch/libs/Makefile	1970-01-01 00:00:00 +0000
+++ .pc/do_not_build_external_libs.patch/libs/Makefile	2014-04-08 01:47:44 +0000
@@ -0,0 +1,74 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+TOP ?= $(shell ../build/abspath.sh ..)
+MODULE = libs
+
+include $(TOP)/build/Makefile.shell
+
+#-------------------------------------------------------------------------------
+# default
+#
+SUBDIRS = \
+	ext \
+	klib \
+	kproc \
+	kfs \
+	kns \
+	kxml \
+	kfg \
+	krypto \
+	vfs \
+	kapp \
+	kdb \
+	vdb \
+	vxf \
+	search \
+	sraxf \
+	align \
+	axf \
+	wgsxf \
+	ktst \
+	loader \
+	ascp \
+	sra \
+	ncbi-vdb
+
+
+# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
+include $(TOP)/build/Makefile.targets
+
+$(SUBDIRS):
+	@ $(MAKE) -C $@
+
+.PHONY: default $(SUBDIRS)
+
+#-------------------------------------------------------------------------------
+# pass-through
+#
+out debug profile release GCC ICC VC++:
+	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env $@
+
+.PHONY: out debug profile release GCC ICC VC++
 
=== added directory '.pc/hardening-format-security.patch'
=== added directory '.pc/hardening-format-security.patch/libs'
=== added directory '.pc/hardening-format-security.patch/libs/kdb'
=== added file '.pc/hardening-format-security.patch/libs/kdb/database.c'
--- .pc/hardening-format-security.patch/libs/kdb/database.c	1970-01-01 00:00:00 +0000
+++ .pc/hardening-format-security.patch/libs/kdb/database.c	2014-04-08 01:47:44 +0000
@@ -0,0 +1,706 @@
+/*===========================================================================
+*
+*                            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.
+*
+* ===========================================================================
+*
+*/
+
+#define KONST const
+#include <kdb/extern.h>
+#include "database-priv.h"
+#include "dbmgr-priv.h"
+#include "kdb-priv.h"
+#undef KONST
+
+#include <klib/namelist.h>
+#include <klib/log.h>
+#include <klib/rc.h>
+#include <klib/printf.h>
+#include <os-native.h>
+#include <sysalloc.h>
+
+#include <limits.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+
+
+/*--------------------------------------------------------------------------
+ * KDatabase
+ *  connection to a database within file system
+ */
+
+/* GetPath
+ *  return the absolute path to DB
+ */
+LIB_EXPORT rc_t CC KDatabaseGetPath ( KDatabase const *self,
+    const char **path )
+{
+    if ( self == NULL )
+        return RC ( rcDB, rcDatabase, rcAccessing, rcSelf, rcNull );
+    if ( path == NULL )
+        return RC ( rcDB, rcDatabase, rcAccessing, rcParam, rcNull );
+
+    *path = self->path;
+
+    return 0;
+}
+
+/* Whack
+ */
+static
+rc_t KDatabaseWhack ( KDatabase *self )
+{
+    rc_t rc = 0;
+
+    KRefcountWhack ( & self -> refcount, "KDatabase" );
+
+    /* release dad */
+    if ( self -> dad != NULL )
+    {
+        rc = KDatabaseSever ( self -> dad );
+        if ( rc == 0 )
+            self -> dad = NULL;
+    }
+
+    /* remove from mgr */
+    if ( rc == 0 )
+        rc = KDBManagerSever ( self -> mgr );
+
+    /* complete */
+    if ( rc == 0 )
+    {
+        KDirectoryRelease ( self -> dir );
+        free ( self );
+        return 0;
+    }
+
+    KRefcountInit ( & self -> refcount, 1, "KDatabase", "whack", "kdb" );
+
+    return rc;
+}
+
+
+/* AddRef
+ * Release
+ *  all objects are reference counted
+ *  NULL references are ignored
+ */
+LIB_EXPORT rc_t CC KDatabaseAddRef ( const KDatabase *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountAdd ( & self -> refcount, "KDatabase" ) )
+        {
+        case krefLimit:
+            return RC ( rcDB, rcDatabase, rcAttaching, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+LIB_EXPORT rc_t CC KDatabaseRelease ( const KDatabase *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountDrop ( & self -> refcount, "KDatabase" ) )
+        {
+        case krefWhack:
+            return KDatabaseWhack ( ( KDatabase* ) self );
+        case krefNegative:
+            return RC ( rcDB, rcDatabase, rcReleasing, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+/* Sever
+ *  like Release, except called internally
+ *  indicates that a child object is letting go...
+ */
+KDatabase *KDatabaseAttach ( const KDatabase *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountAddDep ( & self -> refcount, "KDatabase" ) )
+        {
+        case krefLimit:
+            return NULL;
+        }
+    }
+    return ( KDatabase* ) self;
+}
+
+rc_t KDatabaseSever ( const KDatabase *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountDropDep ( & self -> refcount, "KDatabase" ) )
+        {
+        case krefWhack:
+            return KDatabaseWhack ( ( KDatabase* ) self );
+        case krefNegative:
+            return RC ( rcDB, rcDatabase, rcReleasing, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+
+/* Make
+ *  make an initialized structure
+ */
+static
+rc_t KDatabaseMake ( KDatabase **dbp, const KDirectory *dir, const char *path )
+{
+    KDatabase *db;
+
+    assert ( dbp != NULL );
+    assert ( path != NULL );
+
+    db = malloc ( sizeof * db + strlen ( path ) );
+    if ( db == NULL )
+    {
+        * dbp = NULL;
+        return RC ( rcDB, rcDatabase, rcConstructing, rcMemory, rcExhausted );
+    }
+
+    db -> mgr = NULL;
+    db -> dad = NULL;
+    db -> dir = dir;
+    KRefcountInit ( & db -> refcount, 1, "KDatabase", "make", path );
+    strcpy ( db -> path, path );
+
+    * dbp = db;
+    return 0;
+}
+
+
+/* OpenDBRead
+ * VOpenDBRead
+ *  open a database for read
+ *
+ *  "db" [ OUT ] - return parameter for newly opened database
+ *
+ *  "path" [ IN ] - NUL terminated string in
+ *  wd-native character set giving path to database
+ */
+static
+rc_t KDBManagerVOpenDBReadInt ( const KDBManager *self, const KDatabase **dbp,
+                                const KDirectory *wd, bool try_srapath,
+                                const char *path, va_list args )
+{
+    rc_t rc;
+
+    /* MUST use vsnprintf because the documented behavior of "path"
+       is that of stdc library's printf, not vdb printf */
+    char dbpath [ 4096 ];
+    int z = ( args == NULL ) ?
+        snprintf ( dbpath, sizeof dbpath, path ):
+        vsnprintf ( dbpath, sizeof dbpath, path, args );
+    if ( z < 0 || ( size_t ) z >= sizeof dbpath )
+        rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcExcessive );
+    else
+    {
+        const KDirectory *dir;
+
+        /* open the directory if its a database */
+        rc = KDBOpenPathTypeRead ( self, wd, dbpath, &dir, kptDatabase, NULL, try_srapath );
+        if ( rc == 0 )
+        {
+            KDatabase *db;
+
+            /* allocate a new guy */
+            rc = KDatabaseMake ( & db, dir, dbpath );
+            if ( rc == 0 )
+            {
+                db -> mgr = KDBManagerAttach ( self );
+                * dbp = db;
+                return 0;
+            }
+
+            KDirectoryRelease ( dir );
+        }
+    }
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KDBManagerOpenDBRead ( const KDBManager *self,
+    const KDatabase **db, const char *path, ... )
+{
+    rc_t rc;
+    va_list args;
+
+    va_start ( args, path );
+    rc = KDBManagerVOpenDBRead ( self, db, path, args );
+    va_end ( args );
+
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KDatabaseOpenDBRead ( const KDatabase *self,
+    const KDatabase **db, const char *name, ... )
+{
+    rc_t rc;
+    va_list args;
+
+    va_start ( args, name );
+    rc = KDatabaseVOpenDBRead ( self, db, name, args );
+    va_end ( args );
+
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KDBManagerVOpenDBRead ( const KDBManager *self,
+    const KDatabase **db, const char *path, va_list args )
+{
+    if ( db == NULL )
+        return RC ( rcDB, rcMgr, rcOpening, rcParam, rcNull );
+
+    * db = NULL;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcMgr, rcOpening, rcSelf, rcNull );
+
+    return KDBManagerVOpenDBReadInt ( self, db, self -> wd, true, path, args );
+}
+
+LIB_EXPORT rc_t CC KDatabaseVOpenDBRead ( const KDatabase *self,
+    const KDatabase **dbp, const char *name, va_list args )
+{
+    rc_t rc;
+    char path [ 256 ];
+
+    if ( dbp == NULL )
+        return RC ( rcDB, rcDatabase, rcOpening, rcParam, rcNull );
+
+    * dbp = NULL;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcDatabase, rcOpening, rcSelf, rcNull );
+
+    rc = KDBVMakeSubPath ( self -> dir,
+        path, sizeof path, "db", 2, name, args );
+    if ( rc == 0 )
+    {
+        rc = KDBManagerVOpenDBReadInt ( self -> mgr, dbp,
+            self -> dir, false, path, NULL );
+        if ( rc == 0 )
+        {
+            KDatabase *db = ( KDatabase* ) * dbp;
+            db -> dad = KDatabaseAttach ( self );
+        }
+    }
+
+    return rc;
+}
+
+
+/* Locked
+ *  returns non-zero if locked
+ */
+LIB_EXPORT bool CC KDatabaseLocked ( const KDatabase *self )
+{
+    rc_t rc;
+
+    if ( self == NULL )
+        return false;
+
+    rc = KDBWritable ( self -> dir, "." );
+    return GetRCState ( rc ) == rcLocked;
+}
+
+/* Exists
+ *  returns true if requested object exists
+ *
+ *  "type" [ IN ] - a KDBPathType
+ *  valid values are kptIndex and kptColumn
+ *
+ *  "path" [ IN ] - NUL terminated path
+ */
+LIB_EXPORT bool CC KDatabaseVExists ( const KDatabase *self, uint32_t type, const char *name, va_list args )
+{
+    if ( self != NULL && name != NULL && name [ 0 ] != 0 )
+    {
+        rc_t rc;
+        size_t len;
+        const char *ns;
+        char path [ 256 ];
+
+        switch ( type )
+        {
+        case kptDatabase:
+            ns = "db";
+            len = 2;
+            break;
+
+        case kptTable:
+            ns = "tbl";
+            len = 3;
+            break;
+
+        case kptIndex:
+            ns = "idx";
+            len = 3;
+            break;
+
+        default:
+            return false;
+        }
+
+        rc = KDBVMakeSubPath ( self -> dir, path, sizeof path, ns, len, name, args );
+        if ( rc == 0 )
+        {
+            switch ( KDirectoryPathType ( self -> dir, path ) )
+            {
+            case kptFile:
+            case kptDir:
+            case kptFile | kptAlias:
+            case kptDir | kptAlias:
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
+LIB_EXPORT bool CC KDatabaseExists ( const KDatabase *self, uint32_t type, const char *name, ... )
+{
+    bool exists;
+
+    va_list args;
+    va_start ( args, name );
+
+    exists = KDatabaseVExists ( self, type, name, args );
+
+    va_end ( args );
+
+    return exists;
+}
+
+
+/* IsAlias
+ *  returns true if object name is an alias
+ *  returns path to fundamental name if it was aliased
+ *
+ *  "type" [ IN ] - a KDBPathType
+ *  valid values are kptDatabase, kptTable and kptIndex
+ *
+ *  "resolved" [ OUT ] and "rsize" [ IN ] - optional output buffer
+ *  for fundamenta object name if "alias" is not a fundamental name, 
+ *
+ *  "name" [ IN ] - NUL terminated object name
+ */
+LIB_EXPORT bool CC KDatabaseIsAlias ( const KDatabase *self, uint32_t type,
+    char *resolved, size_t rsize, const char *name )
+{
+    if ( self != NULL && name != NULL && name [ 0 ] != 0 )
+    {
+        rc_t rc;
+        size_t len;
+        const char *ns;
+        char path [ 256 ];
+
+        switch ( type )
+        {
+        case kptDatabase:
+            ns = "db";
+            len = 2;
+            break;
+
+        case kptTable:
+            ns = "tbl";
+            len = 3;
+            break;
+
+        case kptIndex:
+            ns = "idx";
+            len = 3;
+            break;
+
+        default:
+            return false;
+        }
+
+        rc = KDBMakeSubPath ( self -> dir, path, sizeof path, ns, len, name );
+        if ( rc == 0 )
+        {
+            switch ( KDirectoryPathType ( self -> dir, path ) )
+            {
+            case kptFile | kptAlias:
+            case kptDir | kptAlias:
+                if ( resolved != NULL && rsize != 0 )
+                {
+                    const KDirectory *sub;
+                    rc = KDirectoryOpenDirRead ( self -> dir, & sub, false, ns );
+                    * resolved = 0;
+                    if ( rc != 0 )
+                        PLOGERR ( klogWarn, ( klogWarn, rc, "failed to open subdirectory '$(sub)'", "sub=%s", ns ) );
+                    else
+                    {
+                        rc = KDirectoryResolveAlias ( sub, false, resolved, rsize, name );
+                        KDirectoryRelease ( sub );
+                        if ( rc != 0 )
+                            PLOGERR ( klogWarn, ( klogWarn, rc, "failed to resolve alias '$(alias)'", "alias=%s", name ) );
+                    }
+                }
+                return true;
+            }
+        }
+    }
+
+    if ( resolved != NULL && rsize != 0 )
+        * resolved = 0;
+
+    return false;
+}
+
+
+/* Writable
+ *  returns 0 if object is writable
+ *  or a reason why if not
+ *
+ *  "type" [ IN ] - a KDBPathType
+ *  valid values are kptDatabase, kptTable and kptIndex
+ *
+ *  "path" [ IN ] - NUL terminated path
+ */
+LIB_EXPORT rc_t CC KDatabaseVWritable ( const KDatabase *self, uint32_t type, const char *name, va_list args )
+{
+    /* TBD */
+    return -1;
+}
+
+LIB_EXPORT rc_t CC KDatabaseWritable ( const KDatabase *self, uint32_t type, const char *name, ... )
+{
+    rc_t rc;
+
+    va_list args;
+    va_start ( args, name );
+
+    rc = KDatabaseVWritable ( self, type, name, args );
+
+    va_end ( args );
+
+    return rc;
+}
+
+
+/* OpenManager
+ *  duplicate reference to manager
+ *  NB - returned reference must be released
+ */
+LIB_EXPORT rc_t CC KDatabaseOpenManagerRead ( const KDatabase *self, const KDBManager **mgr )
+{
+    rc_t rc;
+
+    if ( mgr == NULL )
+        rc = RC ( rcDB, rcDatabase, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcDatabase, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            rc = KDBManagerAddRef ( self -> mgr );
+            if ( rc == 0 )
+            {
+                * mgr = self -> mgr;
+                return 0;
+            }
+        }
+
+        * mgr = NULL;
+    }
+
+    return rc;
+}
+
+
+/* OpenParent
+ *  duplicate reference to parent database
+ *  NB - returned reference must be released
+ */
+LIB_EXPORT rc_t CC KDatabaseOpenParentRead ( const KDatabase *self, const KDatabase **par )
+{
+    rc_t rc;
+
+    if ( par == NULL )
+        rc = RC ( rcDB, rcDatabase, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcDatabase, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            rc = KDatabaseAddRef ( self -> dad );
+            if ( rc == 0 )
+            {
+                * par = self -> dad;
+                return 0;
+            }
+        }
+
+        * par = NULL;
+    }
+
+    return rc;
+}
+
+
+/* GetDirectory
+ *  access the directory in use
+ */
+LIB_EXPORT rc_t CC KDatabaseOpenDirectoryRead ( const KDatabase *self, const KDirectory **dir )
+{
+    rc_t rc;
+
+    if ( dir == NULL )
+        rc = RC ( rcDB, rcDatabase, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcDatabase, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            * dir = self -> dir;
+            return KDirectoryAddRef ( * dir );
+        }
+
+        * dir = NULL;
+    }
+
+    return rc;
+}
+
+
+/* ModDate
+ *  get modification date
+ */
+LIB_EXPORT rc_t CC KDatabaseModDate ( const KDatabase *self, KTime_t *mtime )
+{
+    rc_t rc;
+
+    if ( mtime == NULL )
+        rc = RC ( rcDB, rcDatabase, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcDatabase, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            /* HACK ALERT - there needs to be a proper way to record modification times */
+            const KDirectory *dir = self -> dir;
+
+            /* this only tells the last time the table was locked,
+               which may be close to the last time it was modified */
+            rc = KDirectoryDate ( dir, mtime, "lock" );
+            if ( rc == 0 )
+                return 0;
+
+            /* get directory timestamp */
+            rc = KDirectoryDate ( dir, mtime, "." );
+            if ( rc == 0 )
+                return 0;
+        }
+
+        * mtime = 0;
+    }
+
+    return rc;
+}
+
+
+/*--------------------------------------------------------------------------
+ * KNameList
+ */
+
+/* List
+ *  create database listings
+ */
+struct FilterData
+{
+    const KDBManager * mgr;
+    int type;
+};
+
+static
+bool CC KDatabaseListFilter ( const KDirectory *dir, const char *name, void *data_ )
+{
+    struct FilterData * data = data_;
+    return ( KDBOpenPathTypeRead ( data->mgr, dir, name, NULL, data->type, NULL, false ) == 0 );
+}
+
+LIB_EXPORT rc_t CC KDatabaseListDB ( const KDatabase *self, KNamelist **names )
+{
+    if ( self != NULL )
+    {
+        struct FilterData data;
+        data.mgr = self->mgr;
+        data.type = kptDatabase;
+
+        return KDirectoryVList ( self -> dir,
+            names, KDatabaseListFilter, &data, "db", NULL );
+    }
+
+    if ( names != NULL )
+        * names = NULL;
+
+    return RC ( rcDB, rcDatabase, rcListing, rcSelf, rcNull );
+}
+
+LIB_EXPORT rc_t CC KDatabaseListTbl ( struct KDatabase const *self, KNamelist **names )
+{
+    if ( self != NULL )
+    {
+        struct FilterData data;
+        data.mgr = self->mgr;
+        data.type = kptTable;
+
+        return KDirectoryVList ( self -> dir,
+            names, KDatabaseListFilter, &data, "tbl", NULL );
+    }
+
+    if ( names != NULL )
+        * names = NULL;
+
+    return RC ( rcDB, rcDatabase, rcListing, rcSelf, rcNull );
+}
+
+LIB_EXPORT rc_t CC KDatabaseListIdx ( struct KDatabase const *self, KNamelist **names )
+{
+    if ( self != NULL )
+    {
+        struct FilterData data;
+        data.mgr = self->mgr;
+        data.type = kptIndex;
+
+        return KDirectoryVList ( self -> dir,
+            names, KDatabaseListFilter, &data, "idx", NULL );
+    }
+
+    if ( names != NULL )
+        * names = NULL;
+
+    return RC ( rcDB, rcDatabase, rcListing, rcSelf, rcNull );
+}
 
=== added file '.pc/hardening-format-security.patch/libs/kdb/index.c'
--- .pc/hardening-format-security.patch/libs/kdb/index.c	1970-01-01 00:00:00 +0000
+++ .pc/hardening-format-security.patch/libs/kdb/index.c	2014-04-08 01:47:44 +0000
@@ -0,0 +1,1006 @@
+/*===========================================================================
+*
+*                            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.
+*
+* ===========================================================================
+*
+*/
+
+#include <kdb/extern.h>
+
+#define KONST const
+#include "index-priv.h"
+#include "dbmgr-priv.h"
+#include "database-priv.h"
+#include "table-priv.h"
+#include "kdb-priv.h"
+#undef KONST
+
+#include <kdb/index.h>
+#include <kfs/file.h>
+#include <kfs/mmap.h>
+#include <klib/refcount.h>
+#include <klib/rc.h>
+#include <os-native.h>
+#include <sysalloc.h>
+
+#include <limits.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <byteswap.h>
+#include <assert.h>
+
+/*--------------------------------------------------------------------------
+ * KIndex
+ *  an object capable of mapping an object to integer oid
+ */
+struct KIndex
+{
+    const KDBManager *mgr;
+    const KDatabase *db;
+    const KTable *tbl;
+    KRefcount refcount;
+    uint32_t vers;
+    union
+    {
+        KTrieIndex_v1 txt1;
+        KTrieIndex_v2 txt234;
+        KU64Index_v3  u64_3;
+    } u;
+    bool converted_from_v1;
+    uint8_t type;
+    char path [ 1 ];
+};
+
+
+/* Whack
+ */
+static
+rc_t KIndexWhack ( KIndex *self )
+{
+    rc_t rc = 0;
+
+    KRefcountWhack ( & self -> refcount, "KIndex" );
+
+    /* release owner */
+    if ( self -> db != NULL )
+    {
+        rc = KDatabaseSever ( self -> db );
+        if ( rc == 0 )
+            self -> db = NULL;
+    }
+    else if ( self -> tbl != NULL )
+    {
+        rc = KTableSever ( self -> tbl );
+        if ( rc == 0 )
+            self -> tbl = NULL;
+    }
+
+    /* remove from mgr */
+    if ( rc == 0 )
+        rc = KDBManagerSever ( self -> mgr );
+    if ( rc == 0 )
+    {
+        self -> mgr = NULL;
+
+        /* complete */
+        rc = SILENT_RC ( rcDB, rcIndex, rcDestroying, rcIndex, rcBadVersion );
+
+        switch ( self -> type )
+        {
+        case kitText:
+        case kitText | kitProj:
+            switch ( self -> vers )
+            {
+            case 1:
+                KTrieIndexWhack_v1 ( & self -> u . txt1 );
+                rc = 0;
+                break;
+            case 2:
+            case 3:
+            case 4:
+                KTrieIndexWhack_v2 ( & self -> u . txt234 );
+                rc = 0;
+                break;
+            }
+            break;
+
+        case kitU64:
+            switch ( self -> vers )
+            {
+            case 3:
+            case 4:
+                rc = KU64IndexWhack_v3 ( & self -> u . u64_3 );
+                break;
+            }
+            break;
+
+        }
+
+        if ( rc == 0 )
+        {
+            free ( self );
+            return 0;
+        }
+    }
+
+    KRefcountInit ( & self -> refcount, 1, "KIndex", "whack", "kidx" );
+    return rc;
+}
+
+
+/* AddRef
+ * Release
+ *  all objects are reference counted
+ *  NULL references are ignored
+ */
+LIB_EXPORT rc_t CC KIndexAddRef ( const KIndex *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountAdd ( & self -> refcount, "KIndex" ) )
+        {
+        case krefLimit:
+            return RC ( rcDB, rcIndex, rcAttaching, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+LIB_EXPORT rc_t CC KIndexRelease ( const KIndex *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountDrop ( & self -> refcount, "KIndex" ) )
+        {
+        case krefWhack:
+            return KIndexWhack ( ( KIndex* ) self );
+        case krefNegative:
+            return RC ( rcDB, rcIndex, rcReleasing, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+
+/* Make
+ */
+static
+rc_t KIndexMake ( KIndex **idxp, const char *path )
+{
+    rc_t rc;
+
+    if ( idxp == NULL )
+        rc = RC ( rcDB, rcIndex, rcCreating, rcParam, rcNull );
+    else
+    {
+        if ( path == NULL )
+            rc = RC ( rcDB, rcIndex, rcCreating, rcPath, rcNull );
+        else if ( path [ 0 ] == 0 )
+            rc = RC ( rcDB, rcIndex, rcCreating, rcPath, rcEmpty );
+        else
+        {
+            KIndex* idx = malloc ( sizeof *idx + strlen ( path ) );
+            if ( idx == NULL )
+                rc = RC ( rcDB, rcIndex, rcConstructing, rcMemory, rcExhausted );
+            else
+            {
+                memset ( idx, 0, sizeof * idx );
+                KRefcountInit ( & idx -> refcount, 1, "KIndex", "make", path );
+                strcpy ( idx -> path, path );
+                * idxp = idx;
+                return 0;
+            }
+        }
+    }
+
+    return rc;
+}
+
+static
+rc_t KIndexAttach ( KIndex *self, const KMMap *mm, bool *byteswap )
+{
+    size_t size;
+    rc_t rc = KMMapSize ( mm, & size );
+    if ( rc == 0 )
+    {
+        const void *addr;
+        rc = KMMapAddrRead ( mm, & addr );
+        if ( rc == 0 )
+        {
+            union
+            {
+                KIndexFileHeader_v1 v1;
+                KIndexFileHeader_v2 v2;
+                KIndexFileHeader_v3 v3;
+            } hdrs;
+
+            const KDBHdr *hdr = addr;
+            const KIndexFileHeader_v3 *fh = addr;
+
+            * byteswap = false;
+            rc = KDBHdrValidate ( hdr, size, 1, KDBINDEXVERS );
+            if ( GetRCState ( rc ) == rcIncorrect && GetRCObject ( rc ) == rcByteOrder )
+            {
+                hdrs . v1 . endian = bswap_32 ( hdr -> endian );
+                hdrs . v1 . version = bswap_32 ( hdr -> version );
+                rc = KDBHdrValidate ( & hdrs . v1, size, 1, KDBINDEXVERS );
+                if ( rc == 0 )
+                {
+                    * byteswap = true;
+                    switch ( hdrs . v1 . version )
+                    {
+                    case 1:
+                        hdr = & hdrs . v1;
+                        break;
+                    case 2:
+                        hdr = & hdrs . v2;
+                        break;
+                    case 3:
+                    case 4:
+                        hdrs . v3 . index_type = bswap_32 ( fh -> index_type );
+                        hdrs . v3 . reserved1 = bswap_32 ( fh -> reserved1 );
+                        hdr = & hdrs . v3 . h;
+                        fh = & hdrs . v3;
+                        break;
+                    }
+                }
+            }
+            if ( rc == 0 )
+            {
+                self -> vers = hdr -> version;
+                switch ( hdr -> version )
+                {
+                case 1:
+#if KDBINDEXVERS != 1
+                    self -> converted_from_v1 = true;
+#endif
+                case 2:
+                    self -> type = kitText;
+                    break;
+                case 3:
+                case 4:
+                {
+                    self -> type = fh -> index_type;
+                    switch ( self -> type )
+                    {
+                    case kitText:
+                    case kitU64:
+                        break;
+                    default:
+                        rc = RC(rcDB, rcIndex, rcConstructing, rcIndex, rcUnrecognized);
+                    }
+                    break;
+                }
+                default:
+                    rc = RC ( rcDB, rcIndex, rcConstructing, rcIndex, rcBadVersion );
+                }
+            }
+        }
+    }
+    return rc;
+}
+
+static
+rc_t KIndexMakeRead ( KIndex **idxp,
+    const KDirectory *dir, const char *path )
+{
+    const KFile *f;
+    rc_t rc = KDirectoryVOpenFileRead ( dir, & f, path, NULL );
+    if ( rc == 0 )
+    {
+        const KMMap *mm;
+        rc = KMMapMakeRead ( & mm, f );
+        if ( rc == 0 )
+        {
+            rc = KIndexMake ( idxp, path );
+            if ( rc == 0 )
+            {
+                bool byteswap;
+                KIndex *idx = * idxp;
+                rc = KIndexAttach ( idx, mm, & byteswap );
+                if ( rc == 0 )
+                {
+                    rc = RC ( rcDB, rcIndex, rcConstructing, rcIndex, rcBadVersion );
+
+                    switch ( idx -> vers )
+                    {
+                    case 1:
+                        /* open using v1 code only if KDBINDEXVERS is 1
+                           if 2 or later, open as a v2 index */
+#if KDBINDEXVERS == 1
+                        rc = KTrieIndexOpen_v1 ( & idx -> u . txt1, mm );
+                        if ( rc == 0 )
+                        {
+                            if ( idx -> u . txt1 . pt . id2node != NULL )
+                                idx -> type = ( uint8_t ) ( kitText | kitProj );
+                            else
+                                idx -> type = ( uint8_t ) kitText;
+                        }
+                        break;
+#else
+                    case 2:
+                        idx -> vers = 3;
+                    case 3:
+                    case 4:
+                        switch ( idx -> type )
+                        {
+                            case kitText:
+                            case kitText | kitProj:
+                                /* will guess version in open */
+                                rc = KTrieIndexOpen_v2 ( & idx -> u . txt234, mm, byteswap );
+                                if( rc == 0 && idx -> u . txt234 . pt . ord2node != NULL )
+                                    idx -> type |= kitProj;
+                                break;
+
+                            case kitU64:
+                                rc = KU64IndexOpen_v3 ( & idx -> u . u64_3, mm, byteswap );
+                                break;
+                        }
+                        break;
+#endif
+                    }
+                }
+
+                if ( rc != 0 )
+                    KIndexWhack ( idx );
+            }
+
+            KMMapRelease ( mm );
+        }
+
+        KFileRelease ( f );
+    }
+    return rc;
+}
+
+
+/* OpenIndexRead
+ * VOpenIndexRead
+ *  open an index for read
+ *
+ *  "idx" [ OUT ] - return parameter for newly opened index
+ *
+ *  "name" [ IN ] - NUL terminated string in UTF-8 giving simple name of idx
+ */
+static
+rc_t KDBManagerOpenIndexReadInt ( const KDBManager *self,
+    KIndex **idxp, const KDirectory *wd, const char *path )
+{
+    char idxpath [ 4096 ];
+    rc_t rc = KDirectoryVResolvePath ( wd, true,
+        idxpath, sizeof idxpath, path, NULL );
+    if ( rc == 0 )
+    {
+        KIndex *idx;
+
+        switch ( KDirectoryVPathType ( wd, idxpath, NULL ) )
+        {
+        case kptNotFound:
+            return RC ( rcDB, rcMgr, rcOpening, rcIndex, rcNotFound );
+        case kptBadPath:
+            return RC ( rcDB, rcMgr, rcOpening, rcPath, rcInvalid );
+        case kptFile:
+        case kptFile | kptAlias:
+            break;
+        default:
+            return RC ( rcDB, rcMgr, rcOpening, rcPath, rcIncorrect );
+        }
+
+        rc = KIndexMakeRead ( & idx, wd, idxpath );
+        if ( rc == 0 )
+        {
+            idx -> mgr = KDBManagerAttach ( self );
+            * idxp = idx;
+            return 0;
+        }
+    }
+    
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KDatabaseOpenIndexRead ( struct KDatabase const *self,
+    const KIndex **idx, const char *name, ... )
+{
+    rc_t rc = 0;
+    va_list args;
+
+    va_start ( args, name );
+    rc = KDatabaseVOpenIndexRead ( self, idx, name, args );
+    va_end ( args );
+
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KDatabaseVOpenIndexRead ( const KDatabase *self,
+    const KIndex **idxp, const char *name, va_list args )
+{
+    rc_t rc = 0;
+    char path [ 256 ];
+
+    if ( idxp == NULL )
+        return RC ( rcDB, rcDatabase, rcOpening, rcParam, rcNull );
+
+    * idxp = NULL;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcDatabase, rcOpening, rcSelf, rcNull );
+
+    rc = KDBVMakeSubPath ( self -> dir,
+        path, sizeof path, "idx", 3, name, args );
+    if ( rc == 0 )
+    {
+        KIndex *idx;
+        rc = KDBManagerOpenIndexReadInt ( self -> mgr,
+            & idx, self -> dir, path );
+        if ( rc == 0 )
+        {
+            idx -> db = KDatabaseAttach ( self );
+            * idxp = idx;
+        }
+    }
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KTableOpenIndexRead ( struct KTable const *self,
+    const KIndex **idx, const char *name, ... )
+{
+    rc_t rc = 0;
+    va_list args;
+
+    va_start ( args, name );
+    rc = KTableVOpenIndexRead ( self, idx, name, args );
+    va_end ( args );
+
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KTableVOpenIndexRead ( const KTable *self,
+    const KIndex **idxp, const char *name, va_list args )
+{
+    rc_t rc = 0;
+    char path [ 256 ];
+
+    if ( idxp == NULL )
+        return RC ( rcDB, rcTable, rcOpening, rcParam, rcNull );
+
+    * idxp = NULL;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcTable, rcOpening, rcSelf, rcNull );
+
+    if ( self -> prerelease )
+    {
+        int len;
+        if ( args == 0 )
+            len = snprintf ( path, sizeof path, name );
+        else
+            len = vsnprintf ( path, sizeof path, name, args );
+        if ( len < 0 || ( size_t ) len >= sizeof path )
+            return RC ( rcDB, rcTable, rcOpening, rcPath, rcExcessive );
+        rc = 0;
+    }
+    else
+    {
+        rc = KDBVMakeSubPath ( self -> dir,
+            path, sizeof path, "idx", 3, name, args );
+    }
+
+    if ( rc == 0 )
+    {
+        KIndex *idx;
+        rc = KDBManagerOpenIndexReadInt ( self -> mgr,
+            & idx, self -> dir, path );
+        if ( rc == 0 )
+        {
+            idx -> tbl = KTableAttach ( self );
+            * idxp = idx;
+        }
+    }
+    return rc;
+}
+
+
+/* Locked
+ *  returns non-zero if locked
+ */
+LIB_EXPORT bool CC KIndexLocked ( const KIndex *self )
+{
+    rc_t rc;
+    const KDirectory *dir;
+
+    if ( self == NULL )
+        return false;
+
+    assert ( self -> db != NULL || self -> tbl != NULL );
+    dir = ( self -> db != NULL ) ?
+        self -> db -> dir : self -> tbl -> dir;
+
+    rc = KDBWritable ( dir, self -> path );
+    return GetRCState ( rc ) == rcLocked;
+}
+
+
+/* Version
+ *  returns the format version
+ */
+LIB_EXPORT rc_t CC KIndexVersion ( const KIndex *self, uint32_t *version )
+{
+    if ( version == NULL )
+        return RC ( rcDB, rcIndex, rcAccessing, rcParam, rcNull );
+
+    if ( self == NULL )
+    {
+        * version = 0;
+        return RC ( rcDB, rcIndex, rcAccessing, rcSelf, rcNull );
+    }
+    
+    * version = self -> vers;
+    return 0;
+}
+
+
+/* Type
+ *  returns the type of index
+ */
+LIB_EXPORT rc_t CC KIndexType ( const KIndex *self, KIdxType *type )
+{
+    if ( type == NULL )
+        return RC ( rcDB, rcIndex, rcAccessing, rcParam, rcNull );
+
+    if ( self == NULL )
+    {
+        * type = ( KIdxType ) 0;
+        return RC ( rcDB, rcIndex, rcAccessing, rcSelf, rcNull );
+    }
+
+    * type = ( KIdxType ) self -> type;
+    return 0;
+}
+
+
+/* CheckConsistency
+ *  run a consistency check on the open index
+ *
+ *  "level" [ IN ] - a measure of rigor of the exercise:
+ *    0 is the lightest
+ *    1 will test all id mappings
+ *    2 will perform key->id retrievals
+ *    3 will perform id->key retrievals if a projection index exists
+ *
+ *  "start_id" [ OUT, NULL OKAY ] - returns the first id in index
+ *
+ *  "id_range" [ OUT, NULL OKAY ] - returns the range of ids from first to last
+ *
+ *  "num_keys" [ OUT, NULL OKAY ] - returns the number of key entries
+ *
+ *  "num_rows" [ OUT, NULL OKAY ] - returns the number of key->id mappings
+ *
+ *  "num_holes" [ OUT, NULL OKAY ] - returns the number of holes in the mapped id range
+ */
+LIB_EXPORT rc_t CC KIndexConsistencyCheck ( const KIndex *self, uint32_t level,
+    int64_t *start_id, uint64_t *id_range, uint64_t *num_keys,
+    uint64_t *num_rows, uint64_t *num_holes )
+{
+    rc_t rc;
+
+    if ( self == NULL )
+        rc = RC ( rcDB, rcIndex, rcValidating, rcSelf, rcNull );
+    else
+    {
+        bool key2id, id2key, all_ids;
+        switch ( level )
+        {
+        case 0:
+            key2id = id2key = all_ids = false;
+            break;
+        case 1:
+            key2id = id2key = false;
+            all_ids = true;
+            break;
+        case 2:
+            key2id = id2key = true;
+            all_ids = false;
+            break;
+        default:
+            key2id = id2key = all_ids = true;
+        }
+
+        switch ( self -> type )
+        {
+        case kitText:
+            id2key = false;
+        case kitText | kitProj:
+            switch ( self -> vers )
+            {
+            case 1:
+                rc = KTrieIndexCheckConsistency_v1 ( & self -> u . txt1,
+                    start_id, id_range, num_keys, num_rows, num_holes,
+                    self, key2id, id2key );
+                break;
+            case 2:
+            case 3:
+            case 4:
+                rc = KTrieIndexCheckConsistency_v2 ( & self -> u . txt234,
+                    start_id, id_range, num_keys, num_rows, num_holes,
+                    self, key2id, id2key, all_ids, self -> converted_from_v1 );
+                break;
+            default:
+                return RC ( rcDB, rcIndex, rcValidating, rcIndex, rcBadVersion );
+            }
+            break;
+
+        default:
+            rc = RC ( rcDB, rcIndex, rcValidating, rcFunction, rcUnsupported );
+        }
+    }
+
+    return rc;
+}
+
+
+/* Find
+ *  finds a single mapping from key
+ */
+LIB_EXPORT rc_t CC KIndexFindText ( const KIndex *self, const char *key, int64_t *start_id, uint64_t *id_count,
+    int ( CC * custom_cmp ) ( const void *item, struct PBSTNode const *n, void *data ),
+    void *data )
+{
+    rc_t rc = 0;
+    uint32_t id32, span;
+
+    if ( id_count != NULL )
+        * id_count = 0;
+
+    if ( start_id == NULL )
+        return RC ( rcDB, rcIndex, rcSelecting, rcParam, rcNull );
+
+    * start_id = 0;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcIndex, rcSelecting, rcSelf, rcNull );
+
+    if ( key == NULL )
+        return RC ( rcDB, rcIndex, rcSelecting, rcString, rcNull );
+    if ( key [ 0 ] == 0 )
+        return RC ( rcDB, rcIndex, rcSelecting, rcString, rcEmpty );
+
+    span = 1;
+
+    switch ( self -> type )
+    {
+    case kitText:
+    case kitText | kitProj:
+        switch ( self -> vers )
+        {
+        case 1:
+            rc = KTrieIndexFind_v1 ( & self -> u . txt1, key, & id32, custom_cmp, data );
+            if ( rc == 0 )
+                * start_id = id32;
+            break;
+        case 2:
+        case 3:
+        case 4:
+#if V2FIND_RETURNS_SPAN
+            rc = KTrieIndexFind_v2 ( & self -> u . txt234, key, start_id, & span, custom_cmp, data, self -> converted_from_v1 );
+#else
+            rc = KTrieIndexFind_v2 ( & self -> u . txt234, key, start_id, custom_cmp, data, self -> converted_from_v1 );
+#endif
+            break;
+        default:
+            return RC ( rcDB, rcIndex, rcSelecting, rcIndex, rcBadVersion );
+        }
+        break;
+    default:
+        return RC ( rcDB, rcIndex, rcSelecting, rcNoObj, rcUnknown );
+    }
+
+    if ( id_count != NULL )
+        * id_count = span;
+    
+    return rc;
+}
+
+
+/* FindAll
+ *  finds all mappings from key
+ */
+LIB_EXPORT rc_t CC KIndexFindAllText ( const KIndex *self, const char *key,
+    rc_t ( CC * f ) ( int64_t id, uint64_t id_count, void *data ), void *data )
+{
+    rc_t rc = 0;
+    int64_t id64;
+    uint32_t id32, span;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcIndex, rcSelecting, rcSelf, rcNull );
+
+    if ( f == NULL )
+        return RC ( rcDB, rcIndex, rcSelecting, rcFunction, rcNull );
+
+    if ( key == NULL )
+        return RC ( rcDB, rcIndex, rcSelecting, rcString, rcNull );
+    if ( key [ 0 ] == 0 )
+        return RC ( rcDB, rcIndex, rcSelecting, rcString, rcEmpty );
+
+    span = 1;
+
+    switch ( self -> type )
+    {
+    case kitText:
+    case kitText | kitProj:
+        switch ( self -> vers )
+        {
+        case 1:
+            rc = KTrieIndexFind_v1 ( & self -> u . txt1, key, & id32, NULL, NULL );
+            if ( rc == 0 )
+                rc = ( * f ) ( id32, 1, data );
+            break;
+        case 2:
+        case 3:
+        case 4:
+#if V2FIND_RETURNS_SPAN
+            rc = KTrieIndexFind_v2 ( & self -> u . txt234, key, & id64, & span, NULL, NULL, self -> converted_from_v1 );
+#else
+            rc = KTrieIndexFind_v2 ( & self -> u . txt234, key, & id64, NULL, NULL, self -> converted_from_v1 );
+#endif
+            if ( rc == 0 )
+                rc = ( * f ) ( id64, span, data );
+            break;
+        default:
+            return RC ( rcDB, rcIndex, rcSelecting, rcIndex, rcBadVersion );
+        }
+        break;
+    default:
+        return RC ( rcDB, rcIndex, rcSelecting, rcNoObj, rcUnknown );
+    }
+    
+    return rc;
+}
+
+
+/* Project
+ *  finds key(s) mapping to value/id if supported
+ */
+LIB_EXPORT rc_t CC KIndexProjectText ( const KIndex *self,
+    int64_t id, int64_t *start_id, uint64_t *id_count,
+    char *key, size_t kmax, size_t *actsize )
+{
+    rc_t rc = 0;
+    int64_t dummy;
+    uint32_t span;
+
+    if ( start_id == NULL )
+        start_id = & dummy;
+
+    * start_id = 0;
+
+    if ( id_count != NULL )
+        * id_count = 0;
+
+    if ( key == NULL && kmax != 0 )
+        return RC ( rcDB, rcIndex, rcProjecting, rcBuffer, rcNull );
+
+    if ( kmax != 0 )
+        key [ 0 ] = 0;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcIndex, rcProjecting, rcSelf, rcNull );
+
+    if ( ( ( KIdxType ) self -> type & kitProj ) == 0 )
+        return RC ( rcDB, rcIndex, rcProjecting, rcIndex, rcIncorrect );
+
+    if ( key == NULL )
+        return RC ( rcDB, rcIndex, rcProjecting, rcBuffer, rcNull );
+
+    span = 1;
+
+    switch ( self -> type )
+    {
+    case kitText | kitProj:
+        switch ( self -> vers )
+        {
+        case 1:
+            /* there is a limit on ids in v1 */
+            if ( id <= 0 || ( id >> 32 ) != 0 )
+                return RC ( rcDB, rcIndex, rcProjecting, rcId, rcNotFound );
+
+            rc = KTrieIndexProject_v1 ( & self -> u . txt1,
+                ( uint32_t ) id, key, kmax, actsize );
+            if ( rc == 0 )
+                * start_id = id;
+            break;
+        case 2:
+        case 3:
+        case 4:
+#if V2FIND_RETURNS_SPAN
+            rc = KTrieIndexProject_v2 ( & self -> u . txt234, id, start_id, & span, key, kmax, actsize );
+#else
+            rc = KTrieIndexProject_v2 ( & self -> u . txt234, id, key, kmax, actsize );
+            if ( rc == 0 )
+                * start_id = id;
+#endif
+            break;
+        default:
+            return RC ( rcDB, rcIndex, rcProjecting, rcIndex, rcBadVersion );
+        }
+        break;
+    default:
+        return RC ( rcDB, rcIndex, rcProjecting, rcNoObj, rcUnknown );
+    }
+
+    if ( id_count != NULL )
+        * id_count = span;
+    
+    return rc;
+}
+
+
+/* ProjectAll
+ *  finds key(s) mapping to value/id if supported
+ */
+LIB_EXPORT rc_t CC KIndexProjectAllText ( const KIndex *self, int64_t id,
+    rc_t ( CC * f ) ( int64_t start_id, uint64_t id_count, const char *key, void *data ),
+    void *data )
+{
+    rc_t rc = 0;
+    char key [ 256 ];
+
+    uint32_t span;
+    int64_t start_id;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcIndex, rcProjecting, rcSelf, rcNull );
+
+    if ( ( ( KIdxType ) self -> type & kitProj ) == 0 )
+        return RC ( rcDB, rcIndex, rcProjecting, rcIndex, rcIncorrect );
+
+    if ( f == NULL )
+        return RC ( rcDB, rcIndex, rcProjecting, rcFunction, rcNull );
+
+    span = 1;
+
+    switch ( self -> type )
+    {
+    case kitText | kitProj:
+        switch ( self -> vers )
+        {
+        case 1:
+            /* there is a limit on ids in v1 */
+            if ( id <= 0 || ( id >> 32 ) != 0 )
+                return RC ( rcDB, rcIndex, rcProjecting, rcId, rcNotFound );
+
+            rc = KTrieIndexProject_v1 ( & self -> u . txt1,
+                ( uint32_t ) id, key, sizeof key, NULL );
+            if ( rc == 0 )
+                rc = ( * f ) ( id, 1, key, data );
+            break;
+
+        case 2:
+        case 3:
+        case 4:
+#if V2FIND_RETURNS_SPAN
+            rc = KTrieIndexProject_v2 ( & self -> u . txt234, id, & start_id, & span, key, sizeof key, NULL );
+#else
+            rc = KTrieIndexProject_v2 ( & self -> u . txt234, start_id = id, key, sizeof key );
+#endif
+            if ( rc == 0 )
+                rc = ( * f ) ( start_id, span, key, data );
+            break;
+            
+        default:
+            return RC ( rcDB, rcIndex, rcProjecting, rcIndex, rcBadVersion );
+        }
+        break;
+    default:
+        return RC ( rcDB, rcIndex, rcProjecting, rcNoObj, rcUnknown );
+    }
+    
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KIndexFindU64( const KIndex* self, uint64_t offset, uint64_t* key, uint64_t* key_size, int64_t* id, uint64_t* id_qty )
+{
+    rc_t rc = 0;
+
+    if( key == NULL || key_size == NULL || id == NULL || id_qty == NULL ) {
+        return RC(rcDB, rcIndex, rcSelecting, rcParam, rcNull);
+    }
+    *key = *key_size = *id = *id_qty = 0;
+    if( self == NULL ) {
+        return RC(rcDB, rcIndex, rcSelecting, rcSelf, rcNull);
+    }
+
+    switch( self->type )
+    {
+    case kitU64:
+        switch( self->vers )
+        {
+        case 3:
+        case 4:
+            rc = KU64IndexFind_v3(&self->u.u64_3, offset, key, key_size, id, id_qty);
+            break;
+        default:
+            return RC(rcDB, rcIndex, rcSelecting, rcIndex, rcBadVersion);
+        }
+        break;
+    default:
+        return RC(rcDB, rcIndex, rcSelecting, rcNoObj, rcUnknown);
+    }
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KIndexFindAllU64( const KIndex* self, uint64_t offset,
+    rc_t ( CC * f )(uint64_t key, uint64_t key_size, int64_t id, uint64_t id_qty, void* data ), void* data)
+{
+    rc_t rc = 0;
+
+    if ( self == NULL )
+        return RC(rcDB, rcIndex, rcSelecting, rcSelf, rcNull);
+    if ( f == NULL )
+        return RC(rcDB, rcIndex, rcSelecting, rcFunction, rcNull);
+
+    switch ( self->type )
+    {
+    case kitU64:
+        switch ( self->vers )
+        {
+        case 3:
+        case 4:
+            rc = KU64IndexFindAll_v3(&self->u.u64_3, offset, f, data);
+            break;
+        default:
+            return RC(rcDB, rcIndex, rcSelecting, rcIndex, rcBadVersion);
+        }
+        break;
+    default:
+        return RC(rcDB, rcIndex, rcSelecting, rcNoObj, rcUnknown);
+    }
+
+    return rc;
+}
+
+
+/* SetMaxId
+ *  certain legacy versions of skey were built to know only the starting id
+ *  of the NAME_FMT column, but were never given a maximum id. allow them
+ *  to be corrected here.
+ */
+LIB_EXPORT void CC KIndexSetMaxRowId ( const KIndex *cself, int64_t max_row_id )
+{
+    if ( cself != NULL ) switch ( cself -> type )
+    {
+    case kitText:
+    case kitText | kitProj:
+        switch ( cself -> vers )
+        {
+        case 2:
+        case 3:
+        case 4:
+            /* here we can repair the max row id */
+            if ( cself -> u . txt234 . pt . maxid < max_row_id )
+                ( ( KIndex* ) cself ) -> u . txt234 . pt . maxid = max_row_id;
+            break;
+        }
+        break;
+    }
+}
 
=== added file '.pc/hardening-format-security.patch/libs/kdb/table.c'
--- .pc/hardening-format-security.patch/libs/kdb/table.c	1970-01-01 00:00:00 +0000
+++ .pc/hardening-format-security.patch/libs/kdb/table.c	2014-04-08 01:47:44 +0000
@@ -0,0 +1,706 @@
+/*===========================================================================
+*
+*                            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.
+*
+* ===========================================================================
+*
+*/
+
+#define TRACK_REFERENCES 0
+
+#define KONST const
+#include "table-priv.h"
+#include "dbmgr-priv.h"
+#include "database-priv.h"
+#include "kdb-priv.h"
+#undef KONST
+
+#include <kdb/extern.h>
+#include <klib/namelist.h>
+#include <klib/log.h>
+#include <klib/rc.h>
+#include <klib/printf.h>
+#include <os-native.h>
+#include <sysalloc.h>
+
+#include <limits.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+
+
+/*--------------------------------------------------------------------------
+ * KTable
+ *  a collection of columns indexed by row id, metadata, indices
+ */
+
+/* GetPath
+ *  return the absolute path to table
+ */
+LIB_EXPORT rc_t CC KTableGetPath ( const KTable *self,
+    const char **path )
+{
+    if ( self == NULL )
+        return RC ( rcDB, rcTable, rcAccessing, rcSelf, rcNull );
+    if ( path == NULL )
+        return RC ( rcDB, rcTable, rcAccessing, rcParam, rcNull );
+
+    *path = self->path;
+
+    return 0;
+}
+
+/* Whack
+ */
+static
+rc_t KTableWhack ( KTable *self )
+{
+    rc_t rc = 0;
+
+    KRefcountWhack ( & self -> refcount, "KTable" );
+
+    if ( self -> db != NULL )
+    {
+        rc = KDatabaseSever ( self -> db );
+        if ( rc == 0 )
+            self -> db = NULL;
+    }
+
+    if ( rc == 0 )
+        rc = KDBManagerSever ( self -> mgr );
+
+    if ( rc == 0 )
+    {
+        KDirectoryRelease ( self -> dir );
+        free ( self );
+        return 0;
+    }
+
+    KRefcountInit ( & self -> refcount, 1, "KTable", "whack", "ktbl" );
+
+    return rc;
+}
+
+
+/* AddRef
+ * Release
+ *  all objects are reference counted
+ *  NULL references are ignored
+ */
+LIB_EXPORT rc_t CC KTableAddRef ( const KTable *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountAdd ( & self -> refcount, "KTable" ) )
+        {
+        case krefLimit:
+            return RC ( rcDB, rcTable, rcAttaching, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+LIB_EXPORT rc_t CC KTableRelease ( const KTable *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountDrop ( & self -> refcount, "KTable" ) )
+        {
+        case krefWhack:
+            return KTableWhack ( ( KTable* ) self );
+        case krefNegative:
+            return RC ( rcDB, rcTable, rcReleasing, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+/* Attach
+ * Sever
+ */
+KTable *KTableAttach ( const KTable *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountAddDep ( & self -> refcount, "KTable" ) )
+        {
+        case krefLimit:
+            return NULL;
+        }
+    }
+    return ( KTable* ) self;
+}
+
+/* Sever
+ *  like KTableRelease, except called internally
+ *  indicates that a child object is letting go...
+ */
+rc_t KTableSever ( const KTable *self )
+{
+    if ( self != NULL )
+    {
+        switch ( KRefcountDropDep ( & self -> refcount, "KTable" ) )
+        {
+        case krefWhack:
+            return KTableWhack ( ( KTable* ) self );
+        case krefNegative:
+            return RC ( rcDB, rcTable, rcReleasing, rcRange, rcExcessive );
+        }
+    }
+    return 0;
+}
+
+/* Make
+ *  make an initialized structure
+ *  NB - does NOT attach reference to dir, but steals it
+ */
+static
+rc_t KTableMake ( KTable **tblp, const KDirectory *dir, const char *path )
+{
+    KTable *tbl;
+
+    assert ( tblp != NULL );
+    assert ( path != NULL );
+
+    tbl = malloc ( sizeof * tbl + strlen ( path ) );
+    if ( tbl == NULL )
+    {
+        * tblp = NULL;
+        return RC ( rcDB, rcTable, rcConstructing, rcMemory, rcExhausted );
+    }
+
+    memset ( tbl, 0, sizeof * tbl );
+    tbl -> dir = dir;
+    KRefcountInit ( & tbl -> refcount, 1, "KTable", "make", path );
+    strcpy ( tbl -> path, path );
+
+    * tblp = tbl;
+    return 0;
+}
+
+
+/* OpenTableRead
+ * VOpenTableRead
+ *  open a table for read
+ *
+ *  "tbl" [ OUT ] - return parameter for newly opened table
+ *
+ *  "path" [ IN ] - NUL terminated string in
+ *  wd-native character set giving path to table
+ */
+static
+rc_t KDBManagerVOpenTableReadInt ( const KDBManager *self,
+    const KTable **tblp, const KDirectory *wd, bool try_srapath,
+    const char *path, va_list args )
+{
+    rc_t rc;
+
+    char tblpath [ 4096 ];
+    int z = ( args == NULL ) ?
+        snprintf ( tblpath, sizeof tblpath, path ):
+        vsnprintf ( tblpath, sizeof tblpath, path, args );
+    if ( z < 0 || ( size_t ) z >= sizeof tblpath )
+        rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcExcessive );
+    else
+    {
+        KTable *tbl;
+        const KDirectory *dir;
+        bool prerelease = false;
+
+        rc = KDBOpenPathTypeRead ( self, wd, tblpath, &dir, kptTable, NULL, try_srapath );
+        if ( rc != 0 )
+        {
+            prerelease = true;
+            rc = KDBOpenPathTypeRead ( self, wd, tblpath, &dir, kptPrereleaseTbl, NULL, try_srapath );
+        }
+
+        if ( rc == 0 )
+        {
+            rc = KTableMake ( & tbl, dir, tblpath );
+            if ( rc == 0 )
+            {
+                tbl -> mgr = KDBManagerAttach ( self );
+                tbl -> prerelease = prerelease;
+                * tblp = tbl;
+                return 0;
+            }
+            KDirectoryRelease ( dir );
+        }
+    }
+    return rc;
+}
+
+
+LIB_EXPORT rc_t CC KDBManagerOpenTableRead ( const KDBManager *self,
+    const KTable **tbl, const char *path, ... )
+{
+    rc_t rc;
+    va_list args;
+
+    va_start ( args, path );
+    rc = KDBManagerVOpenTableRead ( self, tbl, path, args );
+    va_end ( args );
+
+    return rc;
+}
+
+
+LIB_EXPORT rc_t CC KDBManagerVOpenTableRead ( const KDBManager *self,
+    const KTable **tbl, const char *path, va_list args )
+{
+    if ( tbl == NULL )
+        return RC ( rcDB, rcMgr, rcOpening, rcParam, rcNull );
+
+    * tbl = NULL;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcMgr, rcOpening, rcSelf, rcNull );
+
+    return KDBManagerVOpenTableReadInt ( self, tbl, self -> wd, true, path, args);
+}
+
+LIB_EXPORT rc_t CC KDatabaseOpenTableRead ( const KDatabase *self,
+    const KTable **tbl, const char *name, ... )
+{
+    rc_t rc;
+    va_list args;
+
+    va_start ( args, name );
+    rc = KDatabaseVOpenTableRead ( self, tbl, name, args );
+    va_end ( args );
+
+    return rc;
+}
+
+LIB_EXPORT rc_t CC KDatabaseVOpenTableRead ( const KDatabase *self,
+    const KTable **tblp, const char *name, va_list args )
+{
+    rc_t rc;
+    char path [ 256 ];
+
+    if ( tblp == NULL )
+        return RC ( rcDB, rcDatabase, rcOpening, rcParam, rcNull );
+
+    * tblp = NULL;
+
+    if ( self == NULL )
+        return RC ( rcDB, rcDatabase, rcOpening, rcSelf, rcNull );
+
+    rc = KDBVMakeSubPath ( self -> dir,
+        path, sizeof path, "tbl", 3, name, args );
+    if ( rc == 0 )
+    {
+        rc = KDBManagerVOpenTableReadInt ( self -> mgr, tblp,
+            self -> dir, false, path, NULL );
+        if ( rc == 0 )
+        {
+            KTable *tbl = ( KTable* ) * tblp;
+            tbl -> db = KDatabaseAttach ( self );
+        }
+    }
+
+    return rc;
+}
+
+
+/* Locked
+ *  returns non-zero if locked
+ */
+LIB_EXPORT bool CC KTableLocked ( const KTable *self )
+{
+    rc_t rc;
+
+    if ( self == NULL )
+        return false;
+
+    rc = KDBWritable ( self -> dir, "." );
+    return GetRCState ( rc ) == rcLocked;
+}
+
+
+/* Exists
+ *  returns true if requested object exists
+ *
+ *  "type" [ IN ] - a KDBPathType
+ *
+ *  "path" [ IN ] - NUL terminated path
+ */
+LIB_EXPORT bool CC KTableVExists ( const KTable *self, uint32_t type, const char *name, va_list args )
+{
+    if ( self != NULL && name != NULL && name [ 0 ] != 0 )
+    {
+        rc_t rc;
+        const char *ns;
+        char path [ 256 ];
+
+        switch ( type )
+        {
+        case kptIndex:
+            ns = "idx";
+            break;
+
+        case kptColumn:
+            ns = "col";
+            break;
+
+        default:
+            return false;
+        }
+
+        rc = KDBVMakeSubPath ( self -> dir, path, sizeof path, ns, 3, name, args );
+        if ( rc == 0 )
+        {
+            switch ( KDirectoryPathType ( self -> dir, path ) )
+            {
+            case kptFile:
+            case kptDir:
+            case kptFile | kptAlias:
+            case kptDir | kptAlias:
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
+LIB_EXPORT bool CC KTableExists ( const KTable *self, uint32_t type, const char *name, ... )
+{
+    bool exists;
+
+    va_list args;
+    va_start ( args, name );
+
+    exists = KTableVExists ( self, type, name, args );
+
+    va_end ( args );
+
+    return exists;
+}
+
+
+/* IsAlias
+ *  returns true if object name is an alias
+ *  returns path to fundamental name if it was aliased
+ *
+ *  "type" [ IN ] - a KDBPathType
+ *  valid values are kptIndex and kptColumn
+ *
+ *  "resolved" [ OUT ] and "rsize" [ IN ] - optional output buffer
+ *  for fundamenta object name if "alias" is not a fundamental name, 
+ *
+ *  "name" [ IN ] - NUL terminated object name
+ */
+LIB_EXPORT bool CC KTableIsAlias ( const KTable *self, uint32_t type,
+    char *resolved, size_t rsize, const char *name )
+{
+    if ( self != NULL && name != NULL && name [ 0 ] != 0 )
+    {
+        rc_t rc;
+        const char *ns;
+        char path [ 256 ];
+
+        switch ( type )
+        {
+        case kptIndex:
+            ns = "idx";
+            break;
+
+        case kptColumn:
+            ns = "col";
+            break;
+
+        default:
+            return false;
+        }
+
+        rc = KDBMakeSubPath ( self -> dir, path, sizeof path, ns, 3, name );
+        if ( rc == 0 )
+        {
+            switch ( KDirectoryPathType ( self -> dir, path ) )
+            {
+            case kptFile | kptAlias:
+            case kptDir | kptAlias:
+                if ( resolved != NULL && rsize != 0 )
+                {
+                    const KDirectory *sub;
+                    rc = KDirectoryOpenDirRead ( self -> dir, & sub, false, ns );
+                    * resolved = 0;
+                    if ( rc != 0 )
+                        PLOGERR ( klogWarn, ( klogWarn, rc, "failed to open subdirectory '$(sub)'", "sub=%s", ns ) );
+                    else
+                    {
+                        rc = KDirectoryResolveAlias ( sub, false, resolved, rsize, name );
+                        KDirectoryRelease ( sub );
+                        if ( rc != 0 )
+                            PLOGERR ( klogWarn, ( klogWarn, rc, "failed to resolve alias '$(alias)'", "alias=%s", name ) );
+                    }
+                }
+                return true;
+            }
+        }
+    }
+
+    if ( resolved != NULL && rsize != 0 )
+        * resolved = 0;
+
+    return false;
+}
+
+
+/* Writable
+ *  returns 0 if object is writable
+ *  or a reason why if not
+ *
+ *  "type" [ IN ] - a KDBPathType
+ *  valid values are kptIndex and kptColumn
+ *
+ *  "path" [ IN ] - NUL terminated path
+ */
+LIB_EXPORT rc_t CC KTableVWritable ( const KTable *self, uint32_t type, const char *name, va_list args )
+{
+    /* TBD */
+    return -1;
+}
+
+LIB_EXPORT rc_t CC KTableWritable ( const KTable *self, uint32_t type, const char *name, ... )
+{
+    rc_t rc;
+
+    va_list args;
+    va_start ( args, name );
+
+    rc = KTableVWritable ( self, type, name, args );
+
+    va_end ( args );
+
+    return rc;
+}
+
+
+/* OpenManager
+ *  duplicate reference to manager
+ *  NB - returned reference must be released
+ */
+LIB_EXPORT rc_t CC KTableOpenManagerRead ( const KTable *self, const KDBManager **mgr )
+{
+    rc_t rc;
+
+    if ( mgr == NULL )
+        rc = RC ( rcDB, rcTable, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcTable, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            rc = KDBManagerAddRef ( self -> mgr );
+            if ( rc == 0 )
+            {
+                * mgr = self -> mgr;
+                return 0;
+            }
+        }
+
+        * mgr = NULL;
+    }
+
+    return rc;
+}
+
+
+/* OpenParent
+ *  duplicate reference to parent database
+ *  NB - returned reference must be released
+ */
+LIB_EXPORT rc_t CC KTableOpenParentRead ( const KTable *self, const KDatabase **db )
+{
+    rc_t rc;
+
+    if ( db == NULL )
+        rc = RC ( rcDB, rcTable, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcTable, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            rc = KDatabaseAddRef ( self -> db );
+            if ( rc == 0 )
+            {
+                * db = self -> db;
+                return 0;
+            }
+        }
+
+        * db = NULL;
+    }
+
+    return rc;
+}
+
+
+/* GetDirectory
+ *  access the directory in use
+ */
+LIB_EXPORT rc_t CC KTableOpenDirectoryRead ( const KTable *self, const KDirectory **dir )
+{
+    rc_t rc;
+
+    if ( dir == NULL )
+        rc = RC ( rcDB, rcTable, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcTable, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            * dir = self -> dir;
+            return KDirectoryAddRef ( * dir );
+        }
+
+        * dir = NULL;
+    }
+
+    return rc;
+}
+
+
+/* ModDate
+ *  get modification date
+ */
+LIB_EXPORT rc_t CC KTableModDate ( const KTable *self, KTime_t *mtime )
+{
+    rc_t rc;
+
+    if ( mtime == NULL )
+        rc = RC ( rcDB, rcTable, rcAccessing, rcParam, rcNull );
+    else
+    {
+        if ( self == NULL )
+            rc = RC ( rcDB, rcTable, rcAccessing, rcSelf, rcNull );
+        else
+        {
+            /* HACK ALERT - there needs to be a proper way to record modification times */
+            const KDirectory *dir = self -> dir;
+
+            /* this only tells the last time the table was locked,
+               which may be close to the last time it was modified */
+            rc = KDirectoryDate ( dir, mtime, "lock" );
+            if ( rc == 0 )
+                return 0;
+
+            if ( GetRCState ( rc ) == rcNotFound )
+            {
+                rc = KDirectoryDate ( dir, mtime, "sealed" );
+                if ( rc == 0 )
+                    return 0;
+            }
+
+            /* get directory timestamp */
+            rc = KDirectoryDate ( dir, mtime, "." );
+            if ( rc == 0 )
+                return 0;
+        }
+
+        * mtime = 0;
+    }
+
+    return rc;
+}
+
+
+/*--------------------------------------------------------------------------
+ * KNamelist
+ */
+
+/* List
+ *  create table listings
+ */
+struct FilterData
+{
+    const KDBManager * mgr;
+    int type;
+};
+
+static
+bool CC KDatabaseListFilter ( const KDirectory *dir, const char *name, void *data_ )
+{
+    struct FilterData * data = data_;
+    return ( KDBOpenPathTypeRead ( data->mgr, dir, name, NULL, data->type, NULL, false ) == 0 );
+}
+
+LIB_EXPORT rc_t CC KTableListCol ( const KTable *self, KNamelist **names )
+{
+    if ( self != NULL )
+    {
+        struct FilterData data;
+
+        data.mgr = self->mgr;
+        data.type = kptColumn;
+
+        return KDirectoryVList ( self -> dir,
+            names, KDatabaseListFilter, &data, "col", NULL );
+    }
+
+    if ( names != NULL )
+        * names = NULL;
+
+    return RC ( rcDB, rcTable, rcListing, rcSelf, rcNull );
+}
+
+static
+bool CC KTableListIdxFilter ( const KDirectory *dir, const char *name, void *data )
+{
+    const size_t sz = strlen(name);
+    
+    if (sz > 4 && strcmp(&name[sz - 4], ".md5") == 0)
+        return false;
+    return true;
+}
+
+static
+bool CC KTableListSkeyFilter ( const KDirectory *dir, const char *name, void *data )
+{
+    if ( strcmp ( name, "skey" ) == 0 )
+        return true;
+    return false;
+}
+
+LIB_EXPORT rc_t CC KTableListIdx ( const KTable *self, KNamelist **names )
+{
+    if ( self != NULL )
+    {
+        if ( ! self -> prerelease )
+        {
+            return KDirectoryVList ( self -> dir,
+                names, KTableListIdxFilter, NULL, "idx", NULL );
+        }
+
+        return KDirectoryVList ( self -> dir,
+            names, KTableListSkeyFilter, NULL, ".", NULL );
+    }
+
+    if ( names != NULL )
+        * names = NULL;
+
+    return RC ( rcDB, rcTable, rcListing, rcSelf, rcNull );
+}
 
=== added directory '.pc/hardening.patch'
=== added file '.pc/hardening.patch/Makefile'
--- .pc/hardening.patch/Makefile	1970-01-01 00:00:00 +0000
+++ .pc/hardening.patch/Makefile	2014-04-08 01:47:44 +0000
@@ -0,0 +1,110 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+#-------------------------------------------------------------------------------
+# environment
+#
+TOP ?= $(CURDIR)
+include $(TOP)/build/Makefile.shell
+
+
+#-------------------------------------------------------------------------------
+# default
+#
+SUBDIRS = \
+	libs \
+	tools
+
+# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
+include $(TOP)/build/Makefile.targets
+
+default: $(SUBDIRS)
+
+test: $(SUBDIRS)
+
+$(SUBDIRS) test:
+	@ $(MAKE) -C $@
+
+.PHONY: default $(SUBDIRS) test
+
+#-------------------------------------------------------------------------------
+# all
+#
+$(SUBDIRS_ALL):
+
+#-------------------------------------------------------------------------------
+# std
+#
+$(SUBDIRS_STD):
+
+#-------------------------------------------------------------------------------
+# clean
+#
+clean: clean_test
+
+clean_test:
+
+#-------------------------------------------------------------------------------
+# pass-through targets
+#
+COMPILERS = GCC VC++ CLANG
+ARCHITECTURES = i386 x86_64 sparc32 sparc64
+CONFIG = debug profile release static dynamic
+PUBLISH = scm pubtools
+REPORTS = bindir targdir osdir config compilers architecture architectures
+PASSTHRUS = \
+	out \
+	CC $(COMPILERS) \
+	$(ARCHITECTURES) \
+	$(CONFIG) $(PUBLISH)
+
+$(PASSTHRUS):
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
+
+$(REPORTS):
+	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env $@
+
+.PHONY: $(PASSTHRUS) $(REPORTS)
+
+
+#-------------------------------------------------------------------------------
+# configuration help
+#
+help configure:
+	@ echo "Before initial build, run 'make OUTDIR=<dir> out' from"
+	@ echo "the project root to set the output directory of your builds."
+	@ echo
+	@ echo "To select a compiler, run 'make <comp>' where"
+	@ echo "comp = { "$(COMPILERS)" }."
+	@ echo
+	@ echo "For hosts that support cross-compilation ( only Macintosh today ),"
+	@ echo "you can run 'make <arch>' where arch = { "$(ARCHITECTURES)" }."
+	@ echo
+	@ echo "To set a build configuration, run 'make <config>' where"
+	@ echo "config = { "$(CONFIG)" }."
+	@ echo
+
+.PHONY: help configure
 
=== added directory '.pc/hardening.patch/build'
=== added file '.pc/hardening.patch/build/Makefile.env'
--- .pc/hardening.patch/build/Makefile.env	1970-01-01 00:00:00 +0000
+++ .pc/hardening.patch/build/Makefile.env	2014-04-08 01:47:44 +0000
@@ -0,0 +1,343 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+# pick up dependencies from object directory
+ifdef SRCDIR
+	include $(wildcard *.d)
+endif
+
+# determine shell environment
+include $(TOP)/build/Makefile.shell
+
+# normally build shared and static external libs
+LIBEXT = $(LIBX) $(SHLX)
+
+# normally build static intermediate libs
+ILIBEXT = $(LIBX)
+
+# would normally only build dynamic library modules,
+# but some tools are expecting to be able to static link
+MODEXT = $(LIBX) $(SHLX)
+
+# determine BUILD
+ifeq (,$(BUILD))
+	BUILD = dbg
+endif
+
+# some rules are sensitive to the type of build
+BUILDTYPE = $(BUILD)
+
+# adjust settings for build
+ifeq (dbg,$(BUILD))
+	DEBUG := -D_DEBUGGING
+#	ILIBEXT = $(LIBX) $(SHLX)
+	MODEXT = $(LIBX) $(SHLX)
+endif
+ifeq (rel,$(BUILD))
+	DEBUG := -DNDEBUG
+endif
+ifeq (prof,$(BUILD))
+	DEBUG := -DNDEBUG -D_PROFILING
+endif
+
+# allow for an all-static build
+ifeq (stat,$(LNKG))
+	STATIC = --static
+	LINKAGE := -D_STATIC
+	LIBEXT = $(LIBX)
+	ILIBEXT = $(LIBX)
+	MODEXT = $(LIBX)
+	STAT_OR_DYN = static
+	STATICSYSLIBS := --static-system-libs
+
+else
+	STAT_OR_DYN = dynamic
+endif
+
+LOCAL_OR_REMOTE = local
+
+
+# drop all suffix rules
+.SUFFIXES:
+
+# load OS and COMP specific files
+include $(TOP)/build/Makefile.$(OS)
+include $(TOP)/build/Makefile.$(COMP)
+include $(TOP)/build/Makefile.rules
+
+# external schema modules
+EXT_SCHEMA_MODULES = axf sraxf wgsxf vxf
+READONLY_SCHEMA_LIBS = $(addprefix -d,$(EXT_SCHEMA_MODULES))
+UPDATE_SCHEMA_LIBS = $(addprefix -dw,$(EXT_SCHEMA_MODULES))
+ALWAYS_STATIC_SCHEMA_LIBS = $(addprefix -s,$(EXT_SCHEMA_MODULES))
+
+# full directory paths
+OLD_TARGDIR = $(OUTDIR)/$(OSFLAV)/$(BUILD)/$(TOOLSET)/$(ARCH)
+TARGDIR = $(OUTDIR)/$(OSFLAV)/$(TOOLSET)/$(LNKG)/$(ARCH)/$(BUILD)
+BINDIR = $(TARGDIR)/bin
+ifeq (win,$(OS))
+    # on Windows, place test executables next to .dlls
+    TEST_BINDIR = $(BINDIR)
+else
+    TEST_BINDIR = $(TARGDIR)/test-bin
+endif
+ILIBDIR = $(TARGDIR)/ilib
+LIBDIR = $(TARGDIR)/lib
+MODDIR = $(TARGDIR)/mod
+WMODDIR = $(TARGDIR)/wmod
+OBJDIR = $(TARGDIR)/obj/$(MODULE)
+
+# path to the ncbi sub-directory
+# this is where modules and installed schema files are kept
+ifeq (win,$(OS))
+    # under Windows, we are always relative to binary path
+	NCBIDIR = $(BINDIR)/ncbi
+else
+ifeq (--static,$(STATIC))
+    # in static builds, we are relative to binary path
+    # because the configuration library will be part of tool
+	NCBIDIR = $(BINDIR)/ncbi
+else
+    # in dynamic builds, we are relative to library path
+    # because the configuration library will live there
+	NCBIDIR = $(LIBDIR)/ncbi
+endif
+endif
+
+# make reissue command
+MAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
+    TOP=$(TOP) SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(OBJDIR) -f $(SRCDIR)/Makefile
+
+# directory and link creation
+SUBDIRS = bin test-bin ilib lib
+OUTDIRS = schema
+
+# clean rules
+stdclean:
+	@ -rm -rf $(OBJDIR)
+	@ rm -rf $(addsuffix .*,$(addprefix $(ILIBDIR)/,$(ALL_LIBS))) \
+			$(addsuffix .*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \
+			$(addsuffix .*,$(addprefix $(MODDIR)/,$(ALL_LIBS))) \
+			$(addsuffix .*,$(addprefix $(WMODDIR)/,$(ALL_LIBS))) \
+			$(addsuffix *,$(addprefix $(BINDIR)/,$(ALL_TOOLS) $(ALL_LIBS))) \
+			$(addsuffix *,$(addprefix $(TEST_BINDIR)/,$(ALL_TOOLS) $(TEST_TOOLS)))
+
+# removing symbolic links that point to specific builds
+removelinks:
+	@ test ! -h $(OUTDIR)/schema && rm -rf $(OUTDIR)/schema || true
+	@ rm -f $(addprefix $(OUTDIR)/,$(addsuffix $(BITS),$(SUBDIRS)))
+	@ rm -f $(addprefix $(OUTDIR)/,$(OUTDIRS))
+
+# create all required output directories
+makedirs:
+	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
+
+# build version include files
+vers-includes: makedirs
+	@ $(MAKE_CMD) -s $(TARGDIR)/$@
+
+ifeq (win,$(OS))
+
+# Windows doesn't really support symbolic links
+# we may add them back in when our toolkit is able to create them
+rebuild-dirlinks: makedirs
+	@ true
+else
+
+LNDIRS = $(addprefix ln_,$(SUBDIRS))
+$(LNDIRS):
+	@ ln -s $(TARGDIR)/$(subst ln_,,$@) $(OUTDIR)/$(subst ln_,,$@)$(BITS)
+
+ifdef NOREBUILD_LINKS
+rebuild-dirlinks:
+	@ true
+else
+rebuild-dirlinks: removelinks makedirs $(LNDIRS)
+	@ ln -s $(TOP)/interfaces $(OUTDIR)/schema
+endif
+
+endif
+
+.PHONY: stdclean removelinks makedirs vers-includes rebuild-dirlinks
+
+# configuration targets 
+out:
+	@ echo $(OUTDIR) > $(TOP)/build/OUTDIR.$(BUILD_OS)
+	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
+
+CC:
+	@ echo cc > $(TOP)/build/COMP.$(OS)
+
+GCC:
+	@ echo gcc > $(TOP)/build/COMP.$(OS)
+
+ICC:
+	@ echo icc > $(TOP)/build/COMP.$(OS)
+
+VC++:
+	@ echo vc++ > $(TOP)/build/COMP.$(OS)
+
+CLANG:
+	@ echo clang > $(TOP)/build/COMP.$(OS)
+
+static:
+	@ echo stat > $(TOP)/build/LNKG.$(OS)
+
+dynamic:
+	@ echo dyn > $(TOP)/build/LNKG.$(OS)
+
+debug:
+	@ echo dbg > $(TOP)/build/BUILD.$(OS)
+
+profile: static
+	@ echo prof > $(TOP)/build/BUILD.$(OS)
+
+release:
+	@ echo rel > $(TOP)/build/BUILD.$(OS)
+
+pubtools: release static
+
+bindir:
+	@ echo "$(BINDIR)"
+
+targdir:
+	@ echo "$(TARGDIR)"
+
+osdir:
+	@ echo "$(OUTDIR)/$(OSFLAV)"
+
+compilers:
+	@ echo "$(COMPILERS)"
+
+architectures:
+	@ echo "$(ARCHITECTURES)"
+
+architecture:
+	@ echo "$(ARCH)"
+
+config:
+	@ echo "  current build is $(BUILD_OS) $(STAT_OR_DYN) $(BUILD) $(ARCH) build using $(TOOLSET) tools"
+	@ echo "  output target directory is '$(TARGDIR)'"
+	@ echo
+
+.PHONY: out CC GCC ICC debug profile release bindir report_config
+
+# includes based upon build
+ITF = $(TOP)/interfaces
+OSINC = $(TOP)/interfaces/os
+CCINC = $(TOP)/interfaces/cc
+XTINC = $(TOP)/interfaces/ext
+
+# OS specific source and include dirs
+SRCDIRS_OS = $(SRCDIR)/$(OS)
+INCDIRS_OS = $(OSINC)/$(OS)
+
+# most OS' have a parent type
+ifdef OS_DAD
+
+SRCDIRS_OS += $(SRCDIR)/$(OS_DAD)
+INCDIRS_OS += $(OSINC)/$(OS_DAD)
+
+# some OS' have a grandparent
+ifdef OS_GDAD
+SRCDIRS_OS += $(SRCDIR)/$(OS_GDAD)
+INCDIRS_OS += $(OSINC)/$(OS_GDAD)
+endif
+
+endif
+
+# compiler specific includes
+INCDIRS_COMP = \
+	$(CCINC)/$(COMP)/$(ARCH) \
+	$(CCINC)/$(COMP)
+
+# some compilers have a parent type
+ifdef COMP_DAD
+
+INCDIRS_COMP += \
+	$(CCINC)/$(COMP_DAD)/$(ARCH) \
+	$(CCINC)/$(COMP_DAD)
+
+endif
+
+VPATH = \
+	$(SRCDIR)/$(COMP)/$(ARCH) \
+	$(SRCDIR)/$(COMP) \
+	$(SRCDIRS_OS) \
+	$(SRCDIR)
+
+INCDIRS = \
+	$(addprefix -I,$(SRCDIRS_OS)) \
+	$(addprefix -I,$(SRCDIR) $(ITF)) \
+	$(addprefix -I,$(INCDIRS_COMP)) \
+	$(addprefix -I,$(INCDIRS_OS) $(XTINC)) \
+	-I.
+
+
+# defines that describe os & architecture
+DLLX ?= $(SHLX)
+ARCHDEFS = -D_ARCH_BITS=$(BITS) -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
+
+# default tool parameters
+CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS)
+CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS)
+LDFLAGS = $(DBG) $(PROF) $(CARCH)
+
+#-------------------------------------------------------------------------------
+# runtests
+# 
+# MallocScribble=1 is for catching allocation problems on Mac
+#
+ifeq ($(RUNTESTS_OVERRIDE),)
+runtests: std $(TEST_TOOLS)
+	@ echo "$0 $*"; export LD_LIBRARY_PATH=$(LIBDIR);export MallocScribble=1;\
+	for i in $(TEST_TOOLS);\
+	do\
+		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
+		echo Run $(TEST_BINDIR)/$$i;eval $(RUN_REMOTELY) $(TEST_BINDIR)/$$i;r=$$?; \
+		if [ "$$r" != "0" ] ; then exit $$r; fi; \
+	done
+
+.PHONY: runtests
+endif
+
+#-------------------------------------------------------------------------------
+# buildtests
+# 
+buildtests: std $(TEST_TOOLS) $(SLOW_TEST_TOOLS)
+
+#-------------------------------------------------------------------------------
+# slowtests
+# 
+slowtests: std $(SLOW_TEST_TOOLS)
+	@ echo "$0 $*"; export LD_LIBRARY_PATH=$(LIBDIR);\
+	for i in $(SLOW_TEST_TOOLS);\
+	do\
+		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
+		echo Run $(TEST_BINDIR)/$$i;eval $(TEST_BINDIR)/$$i;r=$$?; \
+		if [ "$$r" != "0" ] ; then exit $$r; fi; \
+	done
+
+.PHONY: slowtests buildtests
 
=== removed file 'CHANGES'
--- CHANGES	2012-01-10 09:06:14 +0000
+++ CHANGES	1970-01-01 00:00:00 +0000
@@ -1,30 +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.
-#
-# ===========================================================================
-
-
-The NCBI SRA Software Development Kit
-Contact: [e-mail]
-
-Release documentation is now being delivered at
-http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
 
=== modified file 'Makefile'
--- Makefile	2012-01-10 09:06:14 +0000
+++ Makefile	2014-04-08 01:47:44 +0000
@@ -37,6 +37,9 @@
 	libs \
 	tools
 
+# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
+include $(TOP)/build/Makefile.targets
+
 default: $(SUBDIRS)
 
 test: $(SUBDIRS)
@@ -47,69 +50,44 @@
 .PHONY: default $(SUBDIRS) test
 
 #-------------------------------------------------------------------------------
-# static vs. dynamic
-#
-static:
-	@ touch "$(CURDIR)/build/STATIC"
-
-dynamic:
-	@ rm -f "$(CURDIR)/build/STATIC"
-
-.PHONY: static dynamic
-
-#-------------------------------------------------------------------------------
 # all
 #
-SUBDIRS_ALL = $(addsuffix _all,$(SUBDIRS))
-
-all: $(SUBDIRS_ALL)
-
 $(SUBDIRS_ALL):
-	@ $(MAKE) -C $(subst _all,,$@) all
-
-.PHONY: all $(SUBDIRS_ALL)
 
 #-------------------------------------------------------------------------------
 # std
 #
-SUBDIRS_STD = $(addsuffix _std,$(SUBDIRS))
-
-std: $(SUBDIRS_STD)
-
 $(SUBDIRS_STD):
-	@ $(MAKE) -C $(subst _std,,$@) std
-
-.PHONY: std $(SUBDIRS_STD)
 
 #-------------------------------------------------------------------------------
 # clean
 #
-SUBDIRS_CLEAN = $(addsuffix _clean,$(SUBDIRS_ALL))
-
-clean: $(SUBDIRS_CLEAN)
-
-$(SUBDIRS_CLEAN):
-	@ $(MAKE) -C $(subst _all_clean,,$@) clean
-
-.PHONY: clean $(SUBDIRS_CLEAN)
-
+clean: clean_test
+
+clean_test:
 
 #-------------------------------------------------------------------------------
 # pass-through targets
 #
-COMPILERS = GCC ICC VC++
-ARCHITECTURES = i386 x86_64
-CONFIG = debug profile release
+COMPILERS = GCC VC++ CLANG
+ARCHITECTURES = i386 x86_64 sparc32 sparc64
+CONFIG = debug profile release static dynamic
+PUBLISH = scm pubtools
+REPORTS = bindir targdir osdir config compilers architecture architectures
 PASSTHRUS = \
-	out bindir \
+	out \
 	CC $(COMPILERS) \
 	$(ARCHITECTURES) \
-	$(CONFIG)
+	$(CONFIG) $(PUBLISH)
 
 $(PASSTHRUS):
-	@ $(MAKE) TOP=$(CURDIR) -f build/Makefile.env $@
-
-.PHONY: $(PASSTHRUS)
+	@ $(MAKE) -s TOP=$(CURDIR) DEB_CFLAGS="$(DEB_CFLAGS)" DEB_LDFLAGS="$(DEB_LDFLAGS)" -f build/Makefile.env $@
+	@ $(MAKE) -s TOP=$(CURDIR) DEB_CFLAGS="$(DEB_CFLAGS)" DEB_LDFLAGS="$(DEB_LDFLAGS)" -f build/Makefile.env rebuild-dirlinks config
+
+$(REPORTS):
+	@ $(MAKE) -s TOP=$(CURDIR) DEB_CFLAGS="$(DEB_CFLAGS)" DEB_LDFLAGS="$(DEB_LDFLAGS)" -f build/Makefile.env $@
+
+.PHONY: $(PASSTHRUS) $(REPORTS)
 
 
 #-------------------------------------------------------------------------------
 
=== modified file 'README'
--- README	2012-01-10 09:06:14 +0000
+++ README	2014-04-08 01:47:44 +0000
@@ -32,26 +32,8 @@
 The SRA Toolkit and SDK from NCBI is a collection of tools and
 libraries for using data in the INSDC Sequence Read Archives.
 
-With this release, NCBI has implemented Compression by Reference, a
-sequence alignment compression process for storing sequence data.
-Currently BAM, Complete Genomics and Illumina export.txt formats
-contain alignment information. Compression by Reference only stores
-the difference in base pairs between sequence data and the segments it
-aligns to.  The decompression process to restore original data such as
-fastq-dump would require fast access to the actual sequences of the
-references. NCBI recommends that SRA users dedicate local disk space
-to store local references downloaded from the NCBI SRA site. Linked
-references should be in a location accessible by the SRA Reader
-software.
-
-Older files in the NCBI system may not have been compressed using
-Compression by Reference.  For more information on how to use
-Reference-based compressed files, download local references, and use
-related tools please refer to Compression by Reference file on the
-NCBI SRA website:
-
-    "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=softwareReadme"
-
+With this release, NCBI has implemented Automatic Remote Access by accession,
+making it possible to access data using NCBI servers without prior download.
 
 For additional information on using and building the toolkit,
 please visit our web site at:
 
=== modified file 'README-WINDOWS.txt'
--- README-WINDOWS.txt	2012-01-10 09:06:14 +0000
+++ README-WINDOWS.txt	2014-04-08 01:47:44 +0000
@@ -29,6 +29,21 @@
 Contact: [e-mail]
 
 
+NOTICE:
+
+  Effective as of release 2.1.8, NCBI is no longer supporting public sources for
+  Windows builds. The sources will still contain everything that we use to build
+  the binaries, but may not build in your environment.
+
+  The reason for this change has to do with dependencies upon third party
+  libraries, which are commonly installed on other platforms, but could be
+  described as "hit and miss" on Windows. When the libraries DO exist, it is
+  difficult to know if they have a correct or compatible calling convention.
+
+  We will continue to distribute pre-built binaries for Windows. You are welcome
+  to try your luck at compiling the sources yourself under Cygwin.
+
+
 ENVIRONMENT:
 
   The Windows build uses the same makefiles as Linux and Mac, and has
 
=== removed file 'README-build'
--- README-build	2012-01-10 09:06:14 +0000
+++ README-build	1970-01-01 00:00:00 +0000
@@ -1,237 +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.
-#
-# ===========================================================================
-
-
-The NCBI SRA ( Sequence Read Archive ) SDK ( Software Development Kit )
-
-
-Contact: [e-mail]
-http://trace.ncbi.nlm.nih.gov/Traces/sra/std
-
-
-This version of the NCBI SRA SDK generates loading and dumping tools with
-their respective libraries for building new and accessing existing runs.
-It may be built with GCC, ICC or Microsoft VC++.
-
-
-REQUIREMENTS:
-
-This software release was designed to run under Linux, MacOSX and Windows
-operating systems on Intel x86-compatible 32 and 64 bit architectures.
-
-  ar                # tested with version 2.15.90
-  bash              # certain scripts require bash
-  make              # GNU make version 3.80 or later
-  gcc, g++          # tested with 4.1.2, but should work with others
-  libz              # version 1
-  libbz2            # version 1
-  libxml2           # tested with version 2.6.7 [Linux and Mac only]
-
-If your system does NOT have libz or libbz2, or if the build fails due to
-missing one of the expected libraries, try running "make all" which will
-attempt to download the sources to libz and libbz2 and build them.
-
-OPTIONS:
-
-Specific versions of ICC are supported as an alternate compiler.
-
-  icc, icpc         # tested with 11.0 (64-bit) and 10.1 (32-bit)
-                    # 32-bit 11.0 does not work
-
-WINDOWS BUILD:
-
-The Windows build uses the same makefiles as Linux and Mac, and has been tested
-under Cygwin. You need to execute Cygwin AFTER sourcing the Microsoft batch file
-from Visual Studio.
-
-
-CONTENTS:
-
-  CHANGES           # describes changes at pertinent levels
-  Makefile          # drives configuration and sub-target builds
-  README
-  README-WINDOWS.txt
-  USAGE
-  build             # holds special makefiles and configuration
-  interfaces        # contains module interfaces, schema, plus
-                      compiler and platform specific includes
-  libs              # sdk library code
-  tools             # toolkit code
-  test              # testing code
-
-
-CONFIGURATION:
-
-There are three configurable parameters:
-  1) BUILD  = 'debug', 'release' etc.
-  2) COMP   = 'GCC' etc.
-  3) OUTDIR = <path-to-binaries-libs-objfiles>
-
-The target architecture is chosen to match your build host. At this
-time, only the Macintosh build will support cross-compilation. In the
-instructions below, x86_64 is the assumed architecture. If your host
-is i386 (32-bit), then you would substitute 32 for paths that contain
-64.
-
-
-BUILD INSTRUCTIONS:
-
-## create output directories and symlinks for first time
-
-  $ OUTDIR=<path-to-output>
-  $ make OUTDIR="$OUTDIR" out
-
-The path in OUTDIR MUST be a full path - relative paths may fail.
-
-## decide upon STATIC or DYNAMIC builds
-#  VDB.2 was designed to make use of dynamic libraries, but
-#  in many environments static builds are more convenient or may even be
-#  required, due to installation restrictions.
-#
-#  THE BUILD DOES NOT CURRENTLY SUPPORT PARALLEL DYNAMIC AND STATIC MODES
-#  if you switch between them, you should perform a "make clean" first.
-
-  $ make static
--OR_
-  $ make dynamic
-
-## if you are using a dynamic build, update LD_LIBRARY_PATH - probably want to put
-# in shell startup ( ensure that libz, libbz2 and libxml2 can be found in your path )
-
-  $ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OUTDIR/lib64"
-
-## the build uses "TOP" as an internal variable
-#  if you have it defined in your shell environment, unset it before making
-
-## build the libraries and binaries
-
-  $ make GCC debug     # optionally set compiler and/or build
-  $ make               # builds libraries and binary executables
-
-The standard make will cause default libraries and tools to be built. Binary
-executables and both shared and static libraries can be found in their
-respective output directories.
-
-If the build fails due to not finding libz or libbz2, try:
-
-  $ make all           # see note above on libraries
-
-
-STATIC BUILD RESULTS:
-
-<OUTDIR>/bin64/         # (bin32 for 32-bit builds)
-  abi-dump              # dump to ABI-native format
-  abi-load              # load from ABI-native format
-  align-info            # retrieve information from cSRA object
-  fastq-dump            # dump to FASTQ format
-  fastq-load            # load from FASTQ format
-  helicos-load          # load from Helicos native format
-  illumina-dump         # dump to Illumina-native format
-  illumina-load         # load from Illumina-native format
-  kar                   # single file archive utility
-  kdbmeta               # access db, table or column metadata
-  rcexplain             # return code display utility
-  sam-dump              # dump to SAM format from cSRA
-  sff-dump              # dumps 454 runs in SFF format
-  sff-load              # load from SFF format
-  sra-dbcc              # consistency checker
-  sra-kar               # sra-specific kar tool
-  sra-stat              # gather run statistics and print to stdout
-  srf-load              # load from SRF format
-  vdb-copy              # tool to copy tables
-  vdb-dump              # dump rows in a textual format
-  vdb-lock              # locks an object against modification
-  vdb-unlock            # unlocks an object
-
-<OUTDIR>/bin64/ncbi     # (bin32 for 32-bit builds)
-  config.kfg            # simple text file for configuring file system
-
-<OUTDIR>/lib64/         # (lib32 for 32-bit builds)
-  libkdb                # static physical layer reading library
-  libkfg                # static configuration library
-  libkfs                # static file system library
-  libklib               # static support library
-  libkproc              # static process synchronization library
-  libkq                 # static cross-thread queue library
-  libksproc             # static single-threaded emulation library
-  libksrch              # static search algorithm library
-  libkxfs               # static XML to filesystem library
-  libkxml               # static XML container support library
-  libload               # static loader tool utility library
-  libsradb              # static API for accessing sra
-  libsrareader          # static reader library
-  libsraschema          # static version of SRA schema
-  libvdb                # static virtual layer reading library
-  libwkdb               # static physical layer update library
-  libwsradb             # static update API for SRA
-  libwvdb               # static virtual layer update library
-
-<OUTDIR>/mod64/         # (mod32 for 32-bit builds)
-  -- empty --
-
-<OUTDIR>/wmod64/        # (wmod32 for 32-bit builds)
-  -- empty --
-
-
-
-DYNAMIC BUILD RESULTS:
-
-<OUTDIR>/bin64/         # (bin32 for 32-bit builds)
-  -- same as static --
-
-<OUTDIR>/bin64/ncbi     # (bin32 for 32-bit builds)
-  -- empty --
-
-<OUTDIR>/lib64/         # (lib32 for 32-bit builds)
-  libkdb                # physical layer reading library
-  libkfg                # configuration library
-  libkfs                # file system library
-  libklib               # support library
-  libkproc              # process synchronization library
-  libkq                 # cross-thread queue library
-  libksproc             # single-threaded emulation library
-  libksrch              # search algorithm library
-  libkxfs               # XML to filesystem library
-  libkxml               # XML container support library
-  libload               # loader tool utility library
-  libsra-schema         # weak-linked sra schema
-  libsradb              # API for accessing sra
-  libsrapath            # weak-link stubs for srapath
-  libsrareader          # reader library
-  libvdb                # virtual layer reading library
-  libwkdb               # physical layer update library
-  libwsradb             # update API for SRA
-  libwvdb               # virtual layer update library
-
-<OUTDIR>/lib64/ncbi     # (lib32 for 32-bit builds)
-  config.kfg            # simple text file for configuring file system
-
-<OUTDIR>/mod64/         # (mod32 for 32-bit builds)
-  libaxf                # cSRA-specific VDB external functions
-  libsraxf              # sra-specific VDB external functions
-  libvxf                # generic VDB external functions
-
-<OUTDIR>/wmod64/        # (wmod32 for 32-bit builds)
-  libwsraxf             # sra-specific VDB external functions for update
-  libwvxf               # update VDB external functions
 
=== added file 'README-build.txt'
--- README-build.txt	1970-01-01 00:00:00 +0000
+++ README-build.txt	2014-04-08 01:47:44 +0000
@@ -0,0 +1,259 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+The NCBI SRA ( Sequence Read Archive ) SDK ( Software Development Kit )
+
+
+Contact: [e-mail]
+http://trace.ncbi.nlm.nih.gov/Traces/sra/std
+
+
+This version of the NCBI SRA SDK generates tools with their respective libraries
+for building new and accessing existing runs. It may be built with GCC.
+
+
+REQUIREMENTS:
+
+This software release was designed to run under Linux, MacOSX and Windows
+operating systems on Intel x86-compatible 32 and 64 bit architectures.
+
+  ar                # tested with version 2.22
+  bash              # certain scripts require bash
+  make              # GNU make version 3.81 or later
+  gcc, g++          # tested with 4.4.2, but should work with others
+  libxml2           # tested with version 2.7.6
+  libcurl           # tested with version 7.27
+
+WINDOWS BUILD:
+
+The Windows build uses the same make files as Linux and Mac, and has been tested
+under Cygwin. You need to execute Cygwin AFTER sourcing the Microsoft batch file
+from Visual Studio.
+
+
+CONTENTS:
+
+  Makefile          # drives configuration and sub-target builds
+  README
+  README-WINDOWS.txt
+  build             # holds special makefiles and configuration
+  interfaces        # contains module interfaces, schema, plus
+                      compiler and platform specific includes
+  libs              # sdk library code
+  tools             # toolkit code
+
+
+CONFIGURATION:
+
+There are three configurable parameters:
+  1) BUILD  = 'debug', 'release' etc.
+  2) COMP   = 'GCC' etc.
+  3) OUTDIR = <path-to-binaries-libs-objfiles>
+
+The target architecture is chosen to match your build host. At this
+time, only the Macintosh build will support cross-compilation. In the
+instructions below, x86_64 is the assumed architecture. If your host
+is i386 (32-bit), then you would substitute 32 for paths that contain
+64.
+
+Running "make help" will list more details of how your build may
+be configured:
+
+  Before initial build, run 'make OUTDIR=<dir> out' from
+  the project root to set the output directory of your builds.
+
+  To select a compiler, run 'make <comp>' where
+  comp = { GCC VC++ CLANG }.
+
+  For hosts that support cross-compilation ( only Macintosh today ),
+  you can run 'make <arch>' where arch = { i386 x86_64 sparc32 sparc64 }.
+
+  To set a build configuration, run 'make <config>' where
+  config = { debug profile release static dynamic }.
+
+Running "make config" will show the current configuration, e.g.:
+
+  current build is linux static rel x86_64 build using gcc tools
+  output target directory is '$PATH_TO_OUTPUT/linux/gcc/stat/x86_64/rel'
+
+where "$PATH_TO_OUTPUT" is local to your system, of course.
+
+
+BUILD INSTRUCTIONS:
+
+## create output directories and symlinks for first time
+
+  $ OUTDIR=<path-to-output>
+  $ make OUTDIR="$OUTDIR" out
+
+The path in OUTDIR MUST be a full path - relative paths may fail.
+
+## decide upon STATIC or DYNAMIC builds
+#  VDB.2 was designed to make use of dynamic libraries, but
+#  in many environments static builds are more convenient or may even be
+#  required, due to installation restrictions.
+#
+#  THE BUILD DOES NOT CURRENTLY SUPPORT PARALLEL DYNAMIC AND STATIC MODES
+#  if you switch between them, you should perform a "make clean" first.
+
+  $ make static
+-OR_
+  $ make dynamic
+
+## if you are using a dynamic build, update LD_LIBRARY_PATH - probably want to put
+# in shell startup ( ensure that libz, libbz2 and libxml2 can be found in your path )
+
+  $ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OUTDIR/lib64"
+
+## the build uses "TOP" as an internal variable
+#  if you have it defined in your shell environment, unset it before making
+
+## build the libraries and binaries
+
+  $ make GCC debug     # optionally set compiler and/or build
+  $ make               # builds libraries and binary executables
+
+The standard make will cause default libraries and tools to be built. Binary
+executables and both shared and static libraries can be found in their
+respective output directories.
+
+
+STATIC BUILD RESULTS:
+
+<OUTDIR>/bin64/         # (bin32 for 32-bit builds)
+  abi-dump              # dump to ABI-native format
+  abi-load              # load from ABI-native format
+  align-info            # retrieve information from SRA alignment object (cSRA)
+  bam-load              # load from BAM format into SRA (cSRA)
+  cg-load               # load from Complete Genomics native format
+  fastq-dump            # dump to FASTQ format
+  fastq-load            # load from FASTQ format
+  helicos-load          # load from Helicos native format
+  illumina-dump         # dump to Illumina-native format
+  illumina-load         # load from Illumina-native format
+  kar                   # single file archive utility
+  kdbmeta               # access db, table or column metadata
+  latf-load             # generic FASTQ loader
+  prefetch              # tool to download runs from NCBI by accession
+  rcexplain             # return code display utility
+  sam-dump              # dump to SAM format from cSRA
+  sff-dump              # dumps 454 runs in SFF format
+  sff-load              # load from SFF format
+  sra-kar               # sra-specific kar tool
+  sra-pileup            # produces SAM-style pileup information from SRA (cSRA)
+  sra-sort              # canonically orders SRA (cSRA) data for improved access
+  sra-stat              # gather run statistics and print to stdout
+  srapath               # returns the full location of an object by accession
+  srf-load              # load from SRF format
+  test-sra              # test user's environment for configuration and libraries
+  vdb-config            # display and/or modify user configuration
+  vdb-copy              # tool to copy tables
+  vdb-decrypt           # tool to decrypt files from dbGap
+  vdb-dump              # dump rows in a textual format
+  vdb-encrypt           # to to (re)encrypt files using dbGap encryption key
+  vdb-lock              # locks an object against modification
+  vdb-unlock            # unlocks an object
+
+<OUTDIR>/lib64/         # (lib32 for 32-bit builds)
+  libalign-access       # BAM format reading API
+  libalign-reader       # SRA (cSRA) alignment reading API
+  libbz2                # bzip2 library
+  libkdb                # physical layer reading library
+  libkfg                # configuration library
+  libkfs                # physical file system library
+  libklib               # support library
+  libkproc              # process synchronization library
+  libkq                 # cross-thread queue library
+  libkrypto             # cryptographic library
+  libsproc              # single-threaded stub library
+  libksrch              # search algorithm library
+  libkurl               # interface to libcurl
+  libkxfs               # XML to filesystem library
+  libkxml               # XML container support library
+  libload               # loader tool utility library
+  libsradb              # API for accessing sra
+  libsrareader          # reader library
+  libsraschema          # version of SRA schema for reading
+  libvdb                # virtual layer reading library
+  libvfs                # virtual file system library
+  libwkdb               # physical layer update library
+  libwsradb             # update API for SRA
+  libwsraschema         # version of SRA schema for update
+  libwvdb               # virtual layer update library
+  libz                  # gzip library
+
+<OUTDIR>/mod64/         # (mod32 for 32-bit builds)
+  -- empty --
+
+<OUTDIR>/wmod64/        # (wmod32 for 32-bit builds)
+  -- empty --
+
+
+
+DYNAMIC BUILD RESULTS:
+
+<OUTDIR>/bin64/         # (bin32 for 32-bit builds)
+  -- same as static --
+
+<OUTDIR>/lib64/         # (lib32 for 32-bit builds)
+  libalign-access       # BAM format reading API
+  libalign-reader       # SRA (cSRA) alignment reading API
+  libbz2                # static bzip2 library
+  libkdb                # physical layer reading library
+  libkfg                # configuration library
+  libkfs                # physical file system library
+  libklib               # support library
+  libkproc              # process synchronization library
+  libkq                 # cross-thread queue library
+  libkrypto             # cryptographic library
+  libsproc              # single-threaded stub library
+  libksrch              # search algorithm library
+  libkurl               # interface to libcurl
+  libkxfs               # XML to filesystem library
+  libkxml               # XML container support library
+  libload               # loader tool utility library
+  libsradb              # API for accessing sra
+  libsrareader          # reader library
+  libsraschema          # static version of SRA schema for reading
+  libvdb                # virtual layer reading library
+  libvfs                # virtual file system library
+  libwkdb               # physical layer update library
+  libwsradb             # update API for SRA
+  libwsraschema         # static version of SRA schema for update
+  libwvdb               # virtual layer update library
+  libz                  # static gzip library
+
+<OUTDIR>/mod64/         # (mod32 for 32-bit builds)
+  libaxf                # cSRA-specific VDB external functions
+  libsraxf              # SRA-specific VDB external functions
+  libvxf                # generic VDB external functions
+  libwgsxf              # WGS-specific VDB external functions
+
+<OUTDIR>/wmod64/        # (wmod32 for 32-bit builds)
+  libwaxf               # cSRA-specific VDB external functions for update
+  libwsraxf             # SRA-specific VDB external functions for update
+  libwvxf               # update VDB external functions
+  libwwgsxf             # WGS-specific VDB external functions for update
+
 
=== added file 'README-config.txt'
--- README-config.txt	1970-01-01 00:00:00 +0000
+++ README-config.txt	2014-04-08 01:47:44 +0000
@@ -0,0 +1,58 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+The NCBI SRA ( Sequence Read Archive )
+
+
+Contact: [e-mail]
+http://trace.ncbi.nlm.nih.gov/Traces/sra/std
+
+About configuration-assistant:
+
+  configuration-assistant.perl will help you to configure the SRA tools to be able
+  to access the local reference repository and to download the correct references
+  for a given cSRA file.
+
+To run configuration-assistant on Linux or Mac:
+  - open a shell
+  - change directory to the folder where you extracted the toolkit (cd .../sratoolkit...),
+  - type 'perl configuration-assistant.perl' (without the quotation marks).
+
+
+To run configuration-assistant on Windows:
+
+  - open Command Prompt (Start->Run->cmd.exe),
+  - change directory to the folder where you extracted the toolkit (cd ...\sratoolkit.x.x.x-win64),
+  - type 'perl configuration-assistant.perl' (without the quotation marks).
+
+
+If the following message shows up:
+
+  "'perl' is not recognized as an internal or external command,
+    operable program or batch file."
+
+that means perl is not installed or not installed properly.
+
+Download Perl at ActiveState.com (http://www.activestate.com/activeperl/downloads)
 
=== removed file 'USAGE'
--- USAGE	2012-01-10 09:06:14 +0000
+++ USAGE	1970-01-01 00:00:00 +0000
@@ -1,162 +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.
-#
-# ===========================================================================
-
-
-The NCBI SRA ( Sequence Read Archive ) Toolkit
-
-
-Contact: [e-mail]
-http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
-
-
-For preliminary documentation on tool usage, consult the files within
-the "help" directory.
-
-
-CHANGES:
-
-SRA Toolkit includes new features in sam-dump tool and vdb-dump tools.  
-
-Sam-dump now supports slicing across multiple sequences, and dumping cSRA files to fasta and fastq formats. In addition, sam-dump has three new parameters
--=|--hide-identical              Output '=' if base is identical to reference
---gzip                           Compress output using gzip
---bzip2                          Compress output using bzip2
-
-vdb-dump has two new parameters
--o|--column_enum_short           enumerates columns in short form
--b|--boolean                     defines how boolean's are printed (1,T)
-
-We have combined the functionality of two scripts, config-assistant.perl and reference-assistant.perl into a single script, configuration-assistant.perl that helps users download the correct references for a given cSRA file and configure the user environment for the SRA Toolkit.
-
-DESCRIPTION:
-
- This release includes tools for reading the SRA archive, generally
- by converting individual runs into some commonly used format such as
- fastq. Support for NCBI's Compression by Reference is also included.
-
- "Linux" binaries have been created on CentOS and SuSE Linux
- distributions. They are not guaranteed to work on other
- distributions. In particular, the version of libc.so should be
- compatible. They are specific to the x86-family architectures.
-
- "Windows" binaries have been created using MSVC's (not Cygwin)
- tools. This release includes Win32 binaries. The "*-load" tools
- are not released for "Windows".
-
- "Mac OS X" binaries are available for the x86-family
- architectures. They will NOT run on PPC Macs. The 64-bit binaries
- will run only on OS 10.6. The 32-bit binaries should run on either
- 10.5 or later.
-
-
-CONTENTS:
-
- "abi-dump"            - dump ABI color-space runs into their native format
- "abi-load"            - load ABI color-space runs
- "fastq-dump"          - dump any run of any platform in FASTQ format
- "fastq-load"          - load FASTQ runs
- "helicos-load"        - load HELICOS runs
- "illumina-dump"       - dump Illumina runs into their native format
- "illumina-load"       - load Illumina native runs
- "kar"                 - an archive extraction tool for .sra files
- "kdbmeta"             - display the contents of one or more metadata stores
- "rcexplain"           - print out error string for return codes (RC)
- "refseq-load"         - ( NEW for Linux and Mac ) download a reference
-                         sequence object
- "sff-dump"            - dump 454 runs into SFF format
- "sff-load"            - load 454 SFF runs
- "sra-dbcc"            - check SRA runs
- "sra-dump"            - dump any run in a textual format [see note below]
- "sra-kar"             - creates a single file archive from an SRA run
- "sra-stat"            - display run column statistics
- "srf-load"            - load SRF runs
- "sam-dump"            - dump a cSRA into the SAM-format
- "vdb-copy"            - copy SRA objects
- "vdb-dump"            - display SRA objects in a textual format [see note below]
- "vdb-lock"            - lock an object against modification
- "vdb-unlock"          - unlock an object
- "align-info"          - displays which references a csra-archive uses
- "vdb-config"          - displays the configuration
-
-
-NOTES:
-
- The "sam-dump" tool only works on cSRA's. ( See README-csra )
- The textual dumpers "sra-dump" and "vdb-dump" are provided in this
- release as an aid in visual inspection. It is likely that their
- actual output formatting will be changed in the near future to a
- stricter, more formalized representation[s].
-
- The "help" information will be improved in near future releases, and
- the tool options will become standardized across the set. We will
- also be providing documentation on our web site.
-
- Tool options may change in the next release. Version 1 tool options
- will remain supported wherever possible in order to preserve
- operation of any existing scripts.
-
-
-CAVEATS:
-
- SRA tools are designed to handle very large amounts of data, and are
- not currently oriented toward desktop use. They work well within any
- Unix-like environment, such as Linux or MacOS's BSD shell.
-
- Windows operation presents a few challenges. We have tested our
- binaries under the MS "cmd.exe" shell and Cygwin's bash. Our tools
- know how to accept paths in Windows, Cygwin, POSIX and MinGW
- formats. Internally, all paths are treated as MinGW-style POSIX
- paths, so any information appearing in output will reflect this
- conversion:
-
-   # simple file names
-   SRR012345.sra                   => [NO CHANGE]
-
-   # relative paths
-   win\SRR012345.sra               => win/SRR012345.sra
-
-   # full or drive-relative paths
-   C:\sra\win\SRR012345.sra        => /C/sra/win/SRR012345.sra
-
-   # network paths
-   \\server\sra\SRR012345.sra      => //server/sra/SRR012345.sra
-
-   # POSIX paths
-   /sra/posix/SRR012345.sra        => [NO CHANGE]
-
-   # Cygwin full paths
-   /cygdrive/C/sra/SRR012345.sra   => /C/sra/SRR012345.sra
-
- There are some situations where the software may behave unexpectedly
- due to path conversions. In particular, since Windows does not
- conform to POSIX path conventions, there may be difficulties
- combining network paths with non-network paths, explicitly or
- implicitly. IF YOU HAVE PROBLEMS, we recommend mounting file servers
- as network drives.
-
- If you run the software under Cygwin, you should take care to use
- either relative paths (those that do not begin with '/') or full
- paths that start with "/cygdrive/". The reason is that Cygwin
- provides its own path manipulation, but our tools are not aware of
- which shell they are running under.
 
=== modified file 'build/BUILD.linux'
--- build/BUILD.linux	2012-01-10 09:06:14 +0000
+++ build/BUILD.linux	2014-04-08 01:47:44 +0000
@@ -1,1 +1,1 @@
-pub
+rel
 
=== modified file 'build/BUILD.mac'
--- build/BUILD.mac	2012-01-10 09:06:14 +0000
+++ build/BUILD.mac	2014-04-08 01:47:44 +0000
@@ -1,1 +1,1 @@
-pub
+rel
 
=== modified file 'build/BUILD.win'
--- build/BUILD.win	2012-01-10 09:06:14 +0000
+++ build/BUILD.win	2014-04-08 01:47:44 +0000
@@ -1,1 +1,1 @@
-pub
+rel
 
=== added file 'build/LNKG.linux'
--- build/LNKG.linux	1970-01-01 00:00:00 +0000
+++ build/LNKG.linux	2014-04-08 01:47:44 +0000
@@ -0,0 +1,1 @@
+stat
 
=== added file 'build/LNKG.mac'
--- build/LNKG.mac	1970-01-01 00:00:00 +0000
+++ build/LNKG.mac	2014-04-08 01:47:44 +0000
@@ -0,0 +1,1 @@
+stat
 
=== added file 'build/LNKG.win'
--- build/LNKG.win	1970-01-01 00:00:00 +0000
+++ build/LNKG.win	2014-04-08 01:47:44 +0000
@@ -0,0 +1,1 @@
+stat
 
=== added file 'build/Makefile.clang'
--- build/Makefile.clang	1970-01-01 00:00:00 +0000
+++ build/Makefile.clang	2014-04-08 01:47:44 +0000
@@ -0,0 +1,80 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+
+# compilers
+CC = @ $(TOP)/build/cc.sh $(OS) 'clang -c' \
+	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CFLAGS)" -MD
+CP = @ $(TOP)/build/cc.sh $(OS) 'clang -xc++ -c' \
+	 $(CHECKSUM) --objx $(OBJX) --cflags "$(CPFLAGS)" -MD
+
+# C preprocessor
+PP = gcc -E $(CFLAGS)
+
+# linkers
+LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
+	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
+	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
+
+LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
+	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
+	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
+	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
+
+# tool options
+WARN = -Wall -Wno-variadic-macros -Wno-long-long # -Wconversion
+ifeq (linux,$(OS))
+    NO_ARRAY_BOUNDS_WARNING = -Wno-array-bounds
+endif
+
+ifeq (64,$(BITS))
+	CARCH = -m64
+else
+	CARCH = -m32
+endif
+
+ifeq (prof, $(BUILD))
+	PROF = -pg
+endif
+
+ifeq (dbg, $(BUILD))
+	DBG = -g
+	OPT = $(WARN)
+	NOPT = $(WARN)
+	# GCC seems unable to use c99 without ansi, which
+	# basically clobbers features back to c89. the options
+	# must be specified in the order shown.
+	PED = -std=c99 -ansi -pedantic # -fdiagnostics-show-option
+else
+
+ifeq (x86_64, $(ARCH))
+	OPT = -O3 -Wall -Wno-variadic-macros -fno-strict-aliasing
+else
+	OPT = -O3 -Wno-variadic-macros -fno-strict-aliasing
+endif
+endif
+
+# clang is designed to be a GCC substitute
+COMP_DAD = gcc
 
=== modified file 'build/Makefile.env'
--- build/Makefile.env	2012-01-10 09:06:14 +0000
+++ build/Makefile.env	2014-04-08 01:47:44 +0000
@@ -37,8 +37,9 @@
 # normally build static intermediate libs
 ILIBEXT = $(LIBX)
 
-# only build dynamic library modules
-MODEXT = $(SHLX)
+# would normally only build dynamic library modules,
+# but some tools are expecting to be able to static link
+MODEXT = $(LIBX) $(SHLX)
 
 # determine BUILD
 ifeq (,$(BUILD))
@@ -59,27 +60,24 @@
 endif
 ifeq (prof,$(BUILD))
 	DEBUG := -DNDEBUG -D_PROFILING
-	STATIC = --static
-endif
-ifeq (pub,$(BUILD))
-	DEBUG := -DNDEBUG
-	BUILDTYPE = rel
-	STATIC = --static
-	STATICSYSLIBS := --static-system-libs
-endif
-
+endif
 
 # allow for an all-static build
-ifndef STATIC
-	STATIC = $(shell test -f $(TOP)/build/STATIC && echo "--static")
-endif
-ifeq (--static,$(STATIC))
+ifeq (stat,$(LNKG))
+	STATIC = --static
 	LINKAGE := -D_STATIC
 	LIBEXT = $(LIBX)
 	ILIBEXT = $(LIBX)
 	MODEXT = $(LIBX)
+	STAT_OR_DYN = static
+	STATICSYSLIBS := --static-system-libs
+
+else
+	STAT_OR_DYN = dynamic
 endif
 
+LOCAL_OR_REMOTE = local
+
 
 # drop all suffix rules
 .SUFFIXES:
@@ -89,9 +87,22 @@
 include $(TOP)/build/Makefile.$(COMP)
 include $(TOP)/build/Makefile.rules
 
+# external schema modules
+EXT_SCHEMA_MODULES = axf sraxf wgsxf vxf
+READONLY_SCHEMA_LIBS = $(addprefix -d,$(EXT_SCHEMA_MODULES))
+UPDATE_SCHEMA_LIBS = $(addprefix -dw,$(EXT_SCHEMA_MODULES))
+ALWAYS_STATIC_SCHEMA_LIBS = $(addprefix -s,$(EXT_SCHEMA_MODULES))
+
 # full directory paths
-TARGDIR = $(OUTDIR)/$(OSFLAV)/$(BUILD)/$(COMP)/$(ARCH)
+OLD_TARGDIR = $(OUTDIR)/$(OSFLAV)/$(BUILD)/$(TOOLSET)/$(ARCH)
+TARGDIR = $(OUTDIR)/$(OSFLAV)/$(TOOLSET)/$(LNKG)/$(ARCH)/$(BUILD)
 BINDIR = $(TARGDIR)/bin
+ifeq (win,$(OS))
+    # on Windows, place test executables next to .dlls
+    TEST_BINDIR = $(BINDIR)
+else
+    TEST_BINDIR = $(TARGDIR)/test-bin
+endif
 ILIBDIR = $(TARGDIR)/ilib
 LIBDIR = $(TARGDIR)/lib
 MODDIR = $(TARGDIR)/mod
@@ -116,22 +127,22 @@
 endif
 
 # make reissue command
-MAKE_CMD = $(MAKE) BUILD=$(BUILD) COMP=$(COMP) TOP=$(TOP) \
-	SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(OBJDIR) -f $(SRCDIR)/Makefile
+MAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
+    TOP=$(TOP) SRCDIR=$(SRCDIR) OUTDIR=$(OUTDIR) -C $(OBJDIR) -f $(SRCDIR)/Makefile
 
 # directory and link creation
-SUBDIRS = bin ilib lib mod wmod
+SUBDIRS = bin test-bin ilib lib
 OUTDIRS = schema
 
 # clean rules
 stdclean:
-	@ rm -rf $(OBJDIR)
-	@ rm -f $(addsuffix .vers.h,$(ALL_TOOLS) $(ALL_LIBS)) \
-			$(addsuffix .*,$(addprefix $(ILIBDIR)/,$(ALL_LIBS))) \
+	@ -rm -rf $(OBJDIR)
+	@ rm -rf $(addsuffix .*,$(addprefix $(ILIBDIR)/,$(ALL_LIBS))) \
 			$(addsuffix .*,$(addprefix $(LIBDIR)/,$(ALL_LIBS))) \
 			$(addsuffix .*,$(addprefix $(MODDIR)/,$(ALL_LIBS))) \
 			$(addsuffix .*,$(addprefix $(WMODDIR)/,$(ALL_LIBS))) \
-			$(addsuffix *,$(addprefix $(BINDIR)/,$(ALL_TOOLS) $(ALL_LIBS)))
+			$(addsuffix *,$(addprefix $(BINDIR)/,$(ALL_TOOLS) $(ALL_LIBS))) \
+			$(addsuffix *,$(addprefix $(TEST_BINDIR)/,$(ALL_TOOLS) $(TEST_TOOLS)))
 
 # removing symbolic links that point to specific builds
 removelinks:
@@ -143,6 +154,10 @@
 makedirs:
 	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
 
+# build version include files
+vers-includes: makedirs
+	@ $(MAKE_CMD) -s $(TARGDIR)/$@
+
 ifeq (win,$(OS))
 
 # Windows doesn't really support symbolic links
@@ -155,66 +170,79 @@
 $(LNDIRS):
 	@ ln -s $(TARGDIR)/$(subst ln_,,$@) $(OUTDIR)/$(subst ln_,,$@)$(BITS)
 
+ifdef NOREBUILD_LINKS
+rebuild-dirlinks:
+	@ true
+else
 rebuild-dirlinks: removelinks makedirs $(LNDIRS)
 	@ ln -s $(TOP)/interfaces $(OUTDIR)/schema
-
-endif
-
-.PHONY: stdclean removelinks makedirs rebuild-dirlinks
+endif
+
+endif
+
+.PHONY: stdclean removelinks makedirs vers-includes rebuild-dirlinks
 
 # configuration targets 
 out:
-	 echo $(OUTDIR) > $(TOP)/build/OUTDIR.$(OS)
+	@ echo $(OUTDIR) > $(TOP)/build/OUTDIR.$(BUILD_OS)
 	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
 
 CC:
 	@ echo cc > $(TOP)/build/COMP.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
 
 GCC:
 	@ echo gcc > $(TOP)/build/COMP.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
 
 ICC:
 	@ echo icc > $(TOP)/build/COMP.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
 
 VC++:
 	@ echo vc++ > $(TOP)/build/COMP.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
+
+CLANG:
+	@ echo clang > $(TOP)/build/COMP.$(OS)
+
+static:
+	@ echo stat > $(TOP)/build/LNKG.$(OS)
+
+dynamic:
+	@ echo dyn > $(TOP)/build/LNKG.$(OS)
 
 debug:
 	@ echo dbg > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
 
-profile:
+profile: static
 	@ echo prof > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
 
 release:
 	@ echo rel > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
-
-scm:
-	@ echo scm > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
-
-pubtools:
-	@ echo pub > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
+
+pubtools: release static
 
 bindir:
 	@ echo "$(BINDIR)"
 
-purify:
-	@ echo pur > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
-
-purecov:
-	@ echo pcov > $(TOP)/build/BUILD.$(OS)
-	@ $(MAKE) TOP=$(TOP) -f $(TOP)/build/Makefile.env rebuild-dirlinks
-
-.PHONY: out CC GCC ICC debug profile release scm purify purecov
+targdir:
+	@ echo "$(TARGDIR)"
+
+osdir:
+	@ echo "$(OUTDIR)/$(OSFLAV)"
+
+compilers:
+	@ echo "$(COMPILERS)"
+
+architectures:
+	@ echo "$(ARCHITECTURES)"
+
+architecture:
+	@ echo "$(ARCH)"
+
+config:
+	@ echo "  current build is $(BUILD_OS) $(STAT_OR_DYN) $(BUILD) $(ARCH) build using $(TOOLSET) tools"
+	@ echo "  output target directory is '$(TARGDIR)'"
+	@ echo
+
+.PHONY: out CC GCC ICC debug profile release bindir report_config
 
 # includes based upon build
 ITF = $(TOP)/interfaces
@@ -264,7 +292,8 @@
 	$(addprefix -I,$(SRCDIRS_OS)) \
 	$(addprefix -I,$(SRCDIR) $(ITF)) \
 	$(addprefix -I,$(INCDIRS_COMP)) \
-	$(addprefix -I,$(INCDIRS_OS) $(XTINC))
+	$(addprefix -I,$(INCDIRS_OS) $(XTINC)) \
+	-I.
 
 
 # defines that describe os & architecture
@@ -272,6 +301,43 @@
 ARCHDEFS = -D_ARCH_BITS=$(BITS) -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
 
 # default tool parameters
-CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS)
+CFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS) $(DEB_CFLAGS)
 CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(LINKAGE) $(DEFINES) $(ARCHDEFS) $(INCDIRS)
-LDFLAGS = $(DBG) $(PROF)
+LDFLAGS = $(DBG) $(PROF) $(CARCH) $(DEB_LDFLAGS)
+
+#-------------------------------------------------------------------------------
+# runtests
+# 
+# MallocScribble=1 is for catching allocation problems on Mac
+#
+ifeq ($(RUNTESTS_OVERRIDE),)
+runtests: std $(TEST_TOOLS)
+	@ echo "$0 $*"; export LD_LIBRARY_PATH=$(LIBDIR);export MallocScribble=1;\
+	for i in $(TEST_TOOLS);\
+	do\
+		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
+		echo Run $(TEST_BINDIR)/$$i;eval $(RUN_REMOTELY) $(TEST_BINDIR)/$$i;r=$$?; \
+		if [ "$$r" != "0" ] ; then exit $$r; fi; \
+	done
+
+.PHONY: runtests
+endif
+
+#-------------------------------------------------------------------------------
+# buildtests
+# 
+buildtests: std $(TEST_TOOLS) $(SLOW_TEST_TOOLS)
+
+#-------------------------------------------------------------------------------
+# slowtests
+# 
+slowtests: std $(SLOW_TEST_TOOLS)
+	@ echo "$0 $*"; export LD_LIBRARY_PATH=$(LIBDIR);\
+	for i in $(SLOW_TEST_TOOLS);\
+	do\
+		echo ++++++++++++++++++++++++++++++++++++++++++++++++++++++;\
+		echo Run $(TEST_BINDIR)/$$i;eval $(TEST_BINDIR)/$$i;r=$$?; \
+		if [ "$$r" != "0" ] ; then exit $$r; fi; \
+	done
+
+.PHONY: slowtests buildtests
 
=== modified file 'build/Makefile.gcc'
--- build/Makefile.gcc	2012-01-10 09:06:14 +0000
+++ build/Makefile.gcc	2014-04-08 01:47:44 +0000
@@ -44,7 +44,14 @@
 	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
 
 # tool options
-WARN = -Wall # -Wconversion
+WARN = -Wall -Wno-long-long 
+ifneq (sun,$(OS))
+    WARN += -Wno-variadic-macros
+endif
+
+ifeq (linux,$(OS))
+    NO_ARRAY_BOUNDS_WARNING = -Wno-array-bounds
+endif
 
 ifeq (prof, $(BUILD))
 	PROF = -pg
@@ -54,12 +61,15 @@
 	DBG = -g
 	OPT = $(WARN)
 	NOPT = $(WARN)
-	PED = -std=c99 -ansi -pedantic
+	# GCC seems unable to use c99 without ansi, which
+	# basically clobbers features back to c89. the options
+	# must be specified in the order shown.
+	PED = -std=c99 -ansi -pedantic # -fdiagnostics-show-option
 else
 
 ifeq (x86_64, $(ARCH))
-	OPT = -O3 -fno-strict-aliasing
+	OPT = -O3 -Wall -Wno-variadic-macros -fno-strict-aliasing
 else
-	OPT = -O3 -fno-strict-aliasing
+	OPT = -O3 -Wno-variadic-macros -fno-strict-aliasing
 endif
 endif
 
=== modified file 'build/Makefile.linux'
--- build/Makefile.linux	2011-05-24 14:48:10 +0000
+++ build/Makefile.linux	2014-04-08 01:47:44 +0000
@@ -73,3 +73,10 @@
   endif
 	DFLT_LIBXML_INCLUDES = $(NCBI)/libxml/include/libxml2
 endif
+
+# flex+bison
+LEX  = @ true
+YACC = @ true
+
+# build matrix
+COMPILERS = GCC # ICC
 
=== modified file 'build/Makefile.mac'
--- build/Makefile.mac	2011-05-24 14:48:10 +0000
+++ build/Makefile.mac	2014-04-08 01:47:44 +0000
@@ -68,3 +68,10 @@
 OS_GDAD = unix
 
 LIBXML_LPATH = /usr/lib
+
+# flex+bison: on Mac, use source-controlled generated .c/.h files
+YACC = @ true
+LEX = @ true
+
+# build matrix
+COMPILERS = GCC CLANG
 
=== modified file 'build/Makefile.rules'
--- build/Makefile.rules	2011-05-24 14:48:10 +0000
+++ build/Makefile.rules	2014-04-08 01:47:44 +0000
@@ -99,11 +99,6 @@
 	$(CP) -S -o $@ -fPIC $(NOPT) $<
 
 
-######################################################################
-## TBD: *.vers.h will no longer be generated or used for executables #
-#       instead, we will update the linker to produce a *.vers.o     #
-#       with a stub for KAppVersion to return a constant             #
-######################################################################
 # version include generation
 %.vers.h: %.vers
 	$(TOP)/build/make-vers-inc.sh $^ > $@
 
=== modified file 'build/Makefile.shell'
--- build/Makefile.shell	2012-01-10 09:06:14 +0000
+++ build/Makefile.shell	2014-04-08 01:47:44 +0000
@@ -26,54 +26,72 @@
 # determine OS
 UNAME = $(shell uname -s)
 
-OS = ''
+HOST_OS = ''
 ifeq (Darwin, $(UNAME))
-	OS = mac
+	HOST_OS = mac
 endif
 ifeq (Linux, $(UNAME))
-	OS = linux
+	HOST_OS = linux
 endif
 ifeq (SunOS, $(UNAME))
-	OS = sun
+	HOST_OS = sun
+	ARCHITECTURES = x86_64 i386
 endif
 ifeq (xCYGWIN, $(findstring xCYGWIN,x$(UNAME)))
-	OS = win
+	HOST_OS = win
 endif
 ifeq (xMINGW, $(findstring xMINGW,x$(UNAME)))
-	OS = win
+	HOST_OS = win
 endif
 # handle all other OSes (like BSD or Hurd) as if they were linux (see bug #627861)
-ifeq ($(OS), '')
-	OS = linux
+ifeq ($(HOST_OS), '')
+	HOST_OS = linux
 endif
 
-# OS flavor is normally OS
-OSFLAV = $(OS)
+# assume build OS is the same as host OS
+OS = $(HOST_OS)
+BUILD_OS = $(OS)
 
 # determine ARCH
-ARCH=''
-ifeq (mac,$(OS))
-	ARCH = $(shell $(TOP)/build/mac.arch.sh)
+HOST_ARCH=''
+ARCHITECTURES = default
+ifeq (mac,$(HOST_OS))
+	HOST_ARCH = $(shell $(TOP)/build/mac.arch.sh)
 else
 	MARCH = $(shell uname -m)
 
 	ifeq (i386, $(MARCH))
-		ARCH = i386
+		HOST_ARCH = i386
 	endif
 	ifeq (i486, $(MARCH))
-		ARCH = i386
+		HOST_ARCH = i386
 	endif
 	ifeq (i586, $(MARCH))
-		ARCH = i386
+		HOST_ARCH = i386
 	endif
 	ifeq (i686, $(MARCH))
-		ARCH = i386
+		ifeq (WOW64x, $(findstring WOW64x,$(UNAME)x))
+			# 64-bit capable Cygwin. Analyze the version of cl to set the corect architecture
+			CL = $(shell cl.exe 2>&1 >/dev/null)
+			ifeq (for x64, $(findstring for x64, $(CL)))
+				HOST_ARCH = x86_64
+			else
+				HOST_ARCH = i386
+			endif			
+		else
+			HOST_ARCH = i386
+		endif	
 	endif
 	ifeq (x86_64, $(MARCH))
-		ARCH = x86_64
-	endif
-	ifeq (sun4u,$(MARCH))
-		ARCH = sparc32
+		HOST_ARCH = x86_64
+	endif
+	ifeq (i86pc, $(MARCH))
+		HOST_ARCH = x86_64
+		ARCHITECTURES = x86_64 i386
+	endif
+	ifeq (sun4v,$(MARCH))
+		HOST_ARCH = sparc64
+		ARCHITECTURES = sparc64 sparc32
 	endif
 endif
 # Handle all other architectures equivalent as i386 (see bug #627861)
@@ -81,32 +99,51 @@
 	ARCH = i386
 endif
 
-# determine BITS
-BITS = $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS)
-
-# first pass through defines SRCDIR
-ifndef SRCDIR
-
-# set SRCDIR from MODULE
+ARCH = $(HOST_ARCH)
+REMOTE_ARCH = $(ARCH)
+
+# pick up dependencies from object directory
+ifdef SRCDIR
+	include $(wildcard *.d)
+else
+
+# determine SRCDIR
 ifdef MODULE
 	SRCDIR=$(TOP)/$(MODULE)
 else
 	SRCDIR=$(TOP)
 endif
 
+# set COMP, LNKG and BUILD
+COMP = $(shell test -f $(TOP)/build/COMP && mv $(TOP)/build/COMP $(TOP)/build/COMP.$(OS); test -f $(TOP)/build/COMP.$(OS) && cat $(TOP)/build/COMP.$(OS) || echo gcc)
+LNKG = $(shell test -f $(TOP)/build/STATIC && mv $(TOP)/build/STATIC $(TOP)/build/LNKG.$(OS) && echo stat > $(TOP)/build/LNKG.$(OS); test -f $(TOP)/build/LNKG.$(OS) && cat $(TOP)/build/LNKG.$(OS) || echo stat)
+BUILD = $(shell test -f $(TOP)/build/BUILD && mv $(TOP)/build/BUILD $(TOP)/build/BUILD.$(OS); test -f $(TOP)/build/BUILD.$(OS) && cat $(TOP)/build/BUILD.$(OS) || echo dbg)
+TOOLSET := $(COMP)
+
+ifdef USE_GCC_IF_ICC
+ifeq (icc,$(COMP))
+COMP = gcc
+endif
+ifeq (clang,$(COMP))
+COMP = gcc
+endif
+endif
+
+endif
+
 # set OUTDIR
 ifndef OUTDIR
-	OUTDIR = $(shell test -f $(TOP)/build/OUTDIR.$(OS) && cat $(TOP)/build/OUTDIR.$(OS) || echo $(TOP))
+	OUTDIR = $(shell test -f $(TOP)/build/OUTDIR && mv $(TOP)/build/OUTDIR $(TOP)/build/OUTDIR.$(BUILD_OS); test -f $(TOP)/build/OUTDIR.$(BUILD_OS) && cat $(TOP)/build/OUTDIR.$(BUILD_OS) || echo $(TOP))
 	ifeq (,$(OUTDIR))
 		OUTDIR = $(TOP)
 	endif
-	ifeq (.,$(OUTDIR))
-		OUTDIR = $(TOP)
-	endif
-endif
-
-# set COMP and BUILD
-COMP = $(shell test -f $(TOP)/build/COMP.$(OS) && cat $(TOP)/build/COMP.$(OS) || echo gcc)
-BUILD = $(shell test -f $(TOP)/build/BUILD.$(OS) && cat $(TOP)/build/BUILD.$(OS) || echo dbg)
-
-endif
+endif
+ifeq (,$(ROUTDIR))
+	ROUTDIR = $(RHOME)
+endif
+
+# OS flavor is normally OS
+OSFLAV = $(OS)
+
+# determine BITS
+BITS = $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS)
 
=== added file 'build/Makefile.targets'
--- build/Makefile.targets	1970-01-01 00:00:00 +0000
+++ build/Makefile.targets	2014-04-08 01:47:44 +0000
@@ -0,0 +1,114 @@
+# ===========================================================================
+#
+#                            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.
+#
+# ===========================================================================
+
+# defines make targets commonly used in non-leaf directories:
+#   default
+#   all
+#   std
+#   clean
+#   buildtests
+#   runtests
+#   slowtests