[med-svn] [Git][med-team/staden][master] 4 commits: Enable autoreconf finding all macros and suppress warnings
Andreas Tille
gitlab at salsa.debian.org
Sun Jul 15 08:20:48 BST 2018
Andreas Tille pushed to branch master at Debian Med / staden
Commits:
546cf0a9 by Andreas Tille at 2018-07-15T07:01:11+02:00
Enable autoreconf finding all macros and suppress warnings
- - - - -
0e17cf42 by Andreas Tille at 2018-07-15T07:10:41+02:00
hardening=+all
- - - - -
e18a6c3a by Andreas Tille at 2018-07-15T07:14:10+02:00
Fix spelling
- - - - -
2ce5810c by Andreas Tille at 2018-07-15T07:17:15+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/autoconfig.patch
- debian/patches/fix_implicit_declaration.patch
- debian/patches/series
- + debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,14 +1,15 @@
-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 at debian.org> Sat, 14 Jul 2018 17:31:37 +0200
+ -- Andreas Tille <tille at debian.org> Sun, 15 Jul 2018 07:14:23 +0200
staden (2.0.0+b11-2) unstable; urgency=medium
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,8 +5,6 @@ Uploaders: Tim Booth <tbooth at 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
=====================================
--- /dev/null
+++ b/debian/patches/autoconfig.patch
@@ -0,0 +1,56 @@
+Author: Yavor Doganov <yavor at 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
=====================================
--- a/debian/patches/fix_implicit_declaration.patch
+++ b/debian/patches/fix_implicit_declaration.patch
@@ -1,7 +1,7 @@
Author: Andreas Tille <tille at 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
=====================================
--- a/debian/patches/series
+++ b/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
=====================================
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,93 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at 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
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -1,12 +1,9 @@
#!/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
View it on GitLab: https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f
--
View it on GitLab: https://salsa.debian.org/med-team/staden/compare/9e2d13c25894edf228805a0f18b4efedbdbe87c9...2ce5810c7b40b74c712f3afafb0227535b80742f
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