fix sqlite3

DESCRIPTION

@@ -2,8 +2,8 @@ Package: seqminer
 Type: Package
 Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
         Format and BGEN Format) into R
-Version: 8.3
-Date: 2021-11-7
+Version: 8.4
+Date: 2022-02-5
 Authors@R: c(person("Xiaowei", "Zhan", email = "zhanxw@gmail.com", role = c("aut", "cre")),
            person("Dajiang", "Liu", email = "dajiang.liu@gmail.com", role = "aut"),
            person("Attractive Chaos", email = "attractor@live.co.uk", role = "cph", comment = "We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics."),	

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for seqminer 8.0.
+# Generated by GNU Autoconf 2.69 for seqminer 8.3.
 #
 # Report bugs to <zhanxw@gmail.com>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='seqminer'
 PACKAGE_TARNAME='seqminer'
-PACKAGE_VERSION='8.0'
-PACKAGE_STRING='seqminer 8.0'
+PACKAGE_VERSION='8.3'
+PACKAGE_STRING='seqminer 8.3'
 PACKAGE_BUGREPORT='zhanxw@gmail.com'
 PACKAGE_URL=''
 
@@ -1242,7 +1242,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures seqminer 8.0 to adapt to many kinds of systems.
+\`configure' configures seqminer 8.3 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1304,7 +1304,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of seqminer 8.0:";;
+     short | recursive ) echo "Configuration of seqminer 8.3:";;
    esac
   cat <<\_ACEOF
 
@@ -1384,7 +1384,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-seqminer configure 8.0
+seqminer configure 8.3
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1686,7 +1686,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by seqminer $as_me 8.0, which was
+It was created by seqminer $as_me 8.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2041,6 +2041,10 @@ if test -z "${R_HOME}"; then
    echo "could not determine R_HOME"
    exit 1
 fi
+CC=`"${R_HOME}/bin/R" CMD config CC`
+CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
 
 CC=`"${R_HOME}/bin/R" CMD config CC`
@@ -3092,13 +3096,13 @@ fi
 
 
 LIB_SQLITE=""
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sqlite3_open in -lsqlite" >&5
-$as_echo_n "checking for sqlite3_open in -lsqlite... " >&6; }
-if ${ac_cv_lib_sqlite_sqlite3_open+:} false; then :
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sqlite3_open in -lsqlite3" >&5
+$as_echo_n "checking for sqlite3_open in -lsqlite3... " >&6; }
+if ${ac_cv_lib_sqlite3_sqlite3_open+:} false; then :
   $as_echo_n "(cached) " >&6
 else
   ac_check_lib_save_LIBS=$LIBS
-LIBS="-lsqlite  $LIBS"
+LIBS="-lsqlite3  $LIBS"
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
@@ -3118,17 +3122,17 @@ return sqlite3_open ();
 }
 _ACEOF
 if ac_fn_cxx_try_link "$LINENO"; then :
-  ac_cv_lib_sqlite_sqlite3_open=yes
+  ac_cv_lib_sqlite3_sqlite3_open=yes
 else
-  ac_cv_lib_sqlite_sqlite3_open=no
+  ac_cv_lib_sqlite3_sqlite3_open=no
 fi
 rm -f core conftest.err conftest.$ac_objext \
     conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sqlite_sqlite3_open" >&5
-$as_echo "$ac_cv_lib_sqlite_sqlite3_open" >&6; }
-if test "x$ac_cv_lib_sqlite_sqlite3_open" = xyes; then :
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_sqlite3_sqlite3_open" >&5
+$as_echo "$ac_cv_lib_sqlite3_sqlite3_open" >&6; }
+if test "x$ac_cv_lib_sqlite3_sqlite3_open" = xyes; then :
 
   for ac_header in sqlite3.h
 do :
@@ -3142,7 +3146,7 @@ _ACEOF
 
 $as_echo "#define HAVE_SQLITE 1" >>confdefs.h
 
-    LIB_SQLITE="-lsqlite"
+    LIB_SQLITE="-lsqlite3"
     { $as_echo "$as_me:${as_lineno-$LINENO}: Will use system-wide sqlite library" >&5
 $as_echo "$as_me: Will use system-wide sqlite library" >&6;}
 
@@ -3771,7 +3775,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by seqminer $as_me 8.0, which was
+This file was extended by seqminer $as_me 8.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3833,7 +3837,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-seqminer config.status 8.0
+seqminer config.status 8.3
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -6,6 +6,10 @@ if test -z "${R_HOME}"; then
    echo "could not determine R_HOME"
    exit 1
 fi
+CC=`"${R_HOME}/bin/R" CMD config CC`
+CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
 dnl adopted from: https://github.com/cran/dfmta/blob/master/configure.ac
 AC_DEFUN([AX_GET_R_CONF_VAR],[$1=`"${R_HOME}/bin/R" CMD config $1`])
@@ -58,7 +62,7 @@ AC_CHECK_LIB([sqlite3], [sqlite3_open], [
   AC_CHECK_HEADERS([sqlite3.h], [
     HAVE_SQLITE=1
     AC_DEFINE([HAVE_SQLITE], [1], [Define to 1 if you have sqlite library])
-    LIB_SQLITE="-lsqlite"
+    LIB_SQLITE="-lsqlite3"
     AC_MSG_NOTICE([Will use system-wide sqlite library])
   ])                     
 ], [AC_MSG_NOTICE([Will build sqlite library from the package])])

src/Makevars.in

@@ -85,7 +85,7 @@ endif
 
 ifeq (@HAVE_SQLITE@,1)
 SQLITE_OBJ=
-PKG_LIBS+=-lsqlite
+PKG_LIBS+=-lsqlite3
 else
 SQLITE_OBJ = sqlite/sqlite3.o
 endif