debian/changelog

-staden (2.0.0+b11-3) UNRELEASED; urgency=medium
+staden (2.0.0+b11-3) unstable; urgency=medium
 
   * Fix homepage
   * debhelper 11
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.1.5
-  * Build-Depends: autoconf-archive, pkg-config
-  TODO: This does not help to fix
-     error: possibly undefined macro: AC_MSG_ERROR
+  * Enable autoreconf finding all macros and suppress warnings (thanks to
+    Yavor Doganov for the patch)
+  * hardening=+all
+  * Fix spelling
 
- -- Andreas Tille <tille@debian.org>  Sat, 14 Jul 2018 17:31:37 +0200
+ -- Andreas Tille <tille@debian.org>  Sun, 15 Jul 2018 07:14:23 +0200
 
 staden (2.0.0+b11-2) unstable; urgency=medium
 

debian/control

@@ -5,8 +5,6 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
-               autoconf-archive,
-               pkg-config,
                libstaden-read-dev (>= 1.14.6),
                itcl3-dev,
                itk3-dev,

debian/patches/autoconfig.patch

+Author: Yavor Doganov <yavor@gnu.org>
+Last-Update: Sun, 15 Jul 2018 07:06:40 +0300
+Description: Enable autoreconf finding all macros and suppress warnings
+
+diff --git a/ac_stubs/libcurl_check_config.m4 b/ac_stubs/libcurl_check_config.m4
+index 9b41a73..0c17884 100644
+--- a/ac_stubs/libcurl_check_config.m4
++++ b/ac_stubs/libcurl_check_config.m4
+@@ -116,7 +116,7 @@ AC_DEFUN([LIBCURL_CHECK_CONFIG],
+            	_libcurl_save_libs=$LIBS
+            	LIBS="$LIBCURL $LIBS"
+ 		
+-		AC_LINK_IFELSE(AC_LANG_PROGRAM([#include <curl/curl.h>],[
++		AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[
+ /* Try and use a few common options to force a failure if we are
+    missing symbols or can't link. */
+ int x;
+@@ -127,7 +127,7 @@ x=CURLOPT_FILE;
+ x=CURLOPT_ERRORBUFFER;
+ x=CURLOPT_STDERR;
+ x=CURLOPT_VERBOSE;
+-]),libcurl_cv_lib_curl_only_needs_minus_l_curl=yes,libcurl_cv_lib_curl_only_needs_minus_l_curl=no)
++]])],libcurl_cv_lib_curl_only_needs_minus_l_curl=yes,libcurl_cv_lib_curl_only_needs_minus_l_curl=no)
+ 
+           	CPPFLAGS=$_libcurl_save_cppflags
+            	LIBS=$_libcurl_save_libs
+@@ -178,7 +178,7 @@ x=CURLOPT_VERBOSE;
+            _libcurl_save_libs=$LIBS
+            LIBS="$LIBCURL $LIBS"
+ 
+-           AC_LINK_IFELSE(AC_LANG_PROGRAM([#include <curl/curl.h>],[
++           AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <curl/curl.h>]],[[
+ /* Try and use a few common options to force a failure if we are
+    missing symbols or can't link. */
+ int x;
+@@ -189,7 +189,7 @@ x=CURLOPT_FILE;
+ x=CURLOPT_ERRORBUFFER;
+ x=CURLOPT_STDERR;
+ x=CURLOPT_VERBOSE;
+-]),libcurl_cv_lib_curl_usable=yes,libcurl_cv_lib_curl_usable=no)
++]])],libcurl_cv_lib_curl_usable=yes,libcurl_cv_lib_curl_usable=no)
+ 
+            CPPFLAGS=$_libcurl_save_cppflags
+            LIBS=$_libcurl_save_libs
+diff --git a/configure.in b/configure.in
+index a3ee01b..ddf3f5e 100644
+--- a/configure.in
++++ b/configure.in
+@@ -8,6 +8,7 @@ AC_INIT([staden],[2.0.0b11-2016])
+ 
+ 
+ AC_CONFIG_HEADERS(staden_config.h)
++AC_CONFIG_MACRO_DIR([ac_stubs])
+ 
+ #-----------------------------------------------------------------------------
+ # Checks for compiler programs.

debian/patches/fix_implicit_declaration.patch

 Author: Andreas Tille <tille@debian.org>
 Last-Update: Fri, 27 May 2016 08:58:49 +0200
 Description: Implicite declarations are now breaking the build.
- This patch adds explicite declarations
+ This patch adds explicit declarations
 
 --- a/eba/conf.c
 +++ b/eba/conf.c

debian/patches/series

@@ -5,3 +5,5 @@ enable_setting_stadenroot.patch
 include_xalloc.patch
 use_mkstemp_instead_of_tmpnam.patch
 fix_implicit_declaration.patch
+autoconfig.patch
+spelling.patch

debian/patches/spelling.patch

+Description: Fix spelling
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 14 Jul 2018 17:31:37 +0200
+
+--- a/gap5/export_contigs.c
++++ b/gap5/export_contigs.c
+@@ -864,7 +864,7 @@ static void sam_export_cons_tag(GapIO *i
+ 
+ /*
+  * Exports a single sam sequence, marrying up annotations to the appropriate
+- * sequences and adding these in auxillary tags.
++ * sequences and adding these in auxiliary tags.
+  *
+  * We use the new format PT:Z:<tag_list> for these.
+  *
+--- a/gap5/sam_index.c
++++ b/gap5/sam_index.c
+@@ -19,7 +19,7 @@
+ #include "consensus.h"
+ 
+ /*
+- * Uncomment this if you want sam auxillary tags to be added as tag in
++ * Uncomment this if you want sam auxiliary tags to be added as tag in
+  * gap5.
+  */
+ //#define SAM_AUX_AS_TAG
+@@ -1114,7 +1114,7 @@ int bio_add_unmapped(bam_io_t *bio, bam_
+ 
+     /*
+      * Uncomment one of the two sections below if you wish to allow storing
+-     * sam auxillary records in gap5.
++     * sam auxiliary records in gap5.
+      * This is experimental and the format for these hasn't been finalised
+      * yet.
+      */
+@@ -1237,7 +1237,7 @@ int bio_add_unmapped(bam_io_t *bio, bam_
+     }
+ 
+ #ifdef SAM_AUX_AS_TAG
+-    /* Make an annotation out of the sam auxillary data */
++    /* Make an annotation out of the sam auxiliary data */
+     aux = bam_aux_stringify(b, 1);
+     if (aux && *aux) {
+ 	anno_ele_t *e;
+@@ -1533,7 +1533,7 @@ int bio_del_seq(bam_io_t *bio, pileup_t
+ 
+     /*
+      * Uncomment one of the two sections below if you wish to allow storing
+-     * sam auxillary records in gap5.
++     * sam auxiliary records in gap5.
+      * This is experimental and the format for these hasn't been finalised
+      * yet.
+      */
+@@ -1651,7 +1651,7 @@ int bio_del_seq(bam_io_t *bio, pileup_t
+     }
+ 
+ #ifdef SAM_AUX_AS_TAG
+-    /* Make an annotation out of the sam auxillary data */
++    /* Make an annotation out of the sam auxiliary data */
+     aux = bam_aux_stringify(b, 1);
+     if (aux && *aux) {
+ 	anno_ele_t *e;
+--- a/gap5/tg_iface_g.c
++++ b/gap5/tg_iface_g.c
+@@ -4681,7 +4681,7 @@ static cached_item *io_seq_block_read(vo
+ 	}
+     }
+ 
+-    /* Sam auxillary records */
++    /* Sam auxiliary records */
+     if (sam_aux) {
+ 	for (i = 0; i < SEQ_BLOCK_SZ; i++) {
+ 	    if (!b->seq[i]) continue;
+@@ -4855,7 +4855,7 @@ static int io_seq_block_write(void *dbh,
+ 	memcpy(out[14], s->alignment, s->alignment_len);
+ 	out[14] += s->alignment_len;
+ 
+-	/* Sam auxillary records */
++	/* Sam auxiliary records */
+ 	out[17] += int2u7(s->aux_len, out[17]);
+ 	if (s->aux_len) {
+ 	    memcpy(out[18], s->sam_aux, s->aux_len);
+--- a/gap5/tg_index.c
++++ b/gap5/tg_index.c
+@@ -64,7 +64,7 @@ void usage(void) {
+ /*    fprintf(stderr, "      -V                   Input is AFG (Velvet)format\n"); */
+     fprintf(stderr, "\n");
+     fprintf(stderr, "      -u                   Also store unmapped reads           ({S,B,CR}AM only)\n");
+-    fprintf(stderr, "      -x                   Also store auxillary records        ({S,B,CR}AM only)\n");
++    fprintf(stderr, "      -x                   Also store auxiliary records        ({S,B,CR}AM only)\n");
+     fprintf(stderr, "      -r                   Store reference-position data (on)  ({S,B,CR}AM only)\n");
+     fprintf(stderr, "      -R                   Don't store reference-position data ({S,B,CR}AM only)\n");
+     fprintf(stderr, "      -D                   Do not remove duplicates ({S,B,CR}AM only)\n");

debian/rules

 #!/usr/bin/make -f
 
-# all does not work due to build error with -fpie
-# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 ## DEB_BUILD_ARCH or DEB_BUILD_ARCH_BITS ??
 BITARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-DEB_HOST_MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
 ifeq ($(BITARCH),64)
     enable64bit:=--enable-64bit
 else