[med-svn] [Git][med-team/infernal][master] Fix configure.ac to enable autoreconf
Andreas Tille
gitlab at salsa.debian.org
Mon Jul 16 08:31:01 BST 2018
Andreas Tille pushed to branch master at Debian Med / infernal
Commits:
a9a0482f by Andreas Tille at 2018-07-16T08:34:30+02:00
Fix configure.ac to enable autoreconf
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/autoreconf.patch
- debian/patches/reproducible.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ infernal (1.1.2-2) UNRELEASED; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
+ * Fix configure.ac to enable autoreconf
-- Andreas Tille <tille at debian.org> Wed, 18 Jan 2017 12:56:58 +0100
=====================================
debian/patches/autoreconf.patch
=====================================
--- /dev/null
+++ b/debian/patches/autoreconf.patch
@@ -0,0 +1,141 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 16 Jul 2018 07:59:38 +0200
+Origin: https://lists.debian.org/debian-mentors/2018/07/msg00193.html
+Description: Fix configure.ac to enable autoreconf
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -121,24 +121,24 @@ AC_SUBST(EASEL_VERSION)
+ AC_SUBST(EASEL_URL)
+
+ # Preprocessor symbols (replace #undefs in hmmer/src/p7_config.h and src/config.h)
+-AC_DEFINE_UNQUOTED(INFERNAL_DATE, "$INFERNAL_DATE")
+-AC_DEFINE_UNQUOTED(INFERNAL_COPYRIGHT, "$INFERNAL_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(INFERNAL_LICENSE, "$INFERNAL_LICENSE")
+-AC_DEFINE_UNQUOTED(INFERNAL_VERSION, "$INFERNAL_VERSION")
+-AC_DEFINE_UNQUOTED(INFERNAL_URL, "$INFERNAL_URL")
+-
+-AC_DEFINE_UNQUOTED(HMMER_DATE, "$HMMER_DATE")
+-AC_DEFINE_UNQUOTED(HMMER_COPYRIGHT, "$HMMER_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(HMMER_LICENSE, "$HMMER_LICENSE")
+-AC_DEFINE_UNQUOTED(HMMER_VERSION, "$HMMER_VERSION")
+-AC_DEFINE_UNQUOTED(HMMER_URL, "$HMMER_URL")
+-
+-AC_DEFINE_UNQUOTED(EASEL_DATE, "$EASEL_DATE")
+-AC_DEFINE_UNQUOTED(EASEL_COPYRIGHT, "$EASEL_COPYRIGHT")
+-AC_DEFINE_UNQUOTED(EASEL_LICENSE, "$EASEL_LICENSE")
+-AC_DEFINE_UNQUOTED(EASEL_VERSION, "$EASEL_VERSION")
++AC_DEFINE_UNQUOTED([INFERNAL_DATE], ["$INFERNAL_DATE"], [Timestamp of infernal code])
++AC_DEFINE_UNQUOTED([INFERNAL_COPYRIGHT], ["$INFERNAL_COPYRIGHT"], [Infernal copyright information])
++AC_DEFINE_UNQUOTED([INFERNAL_LICENSE], ["$INFERNAL_LICENSE"], [Infernal license])
++AC_DEFINE_UNQUOTED([INFERNAL_VERSION], ["$INFERNAL_VERSION"], [Invernal version])
++AC_DEFINE_UNQUOTED([INFERNAL_URL], ["$INFERNAL_URL"], [Link to infernal homepage])
++
++AC_DEFINE_UNQUOTED([HMMER_DATE], ["$HMMER_DATE"], [Timestamp of hmmer code])
++AC_DEFINE_UNQUOTED([HMMER_COPYRIGHT], ["$HMMER_COPYRIGHT"], [Hmmer copyright information])
++AC_DEFINE_UNQUOTED([HMMER_LICENSE], ["$HMMER_LICENSE"], [Hmmer license])
++AC_DEFINE_UNQUOTED([HMMER_VERSION], ["$HMMER_VERSION"], [Hmmer version])
++AC_DEFINE_UNQUOTED([HMMER_URL], ["$HMMER_URL"], [Link to hmmer homepage])
++
++AC_DEFINE_UNQUOTED([EASEL_DATE], ["$EASEL_DATE"], [Timestamp of easel code])
++AC_DEFINE_UNQUOTED([EASEL_COPYRIGHT], ["$EASEL_COPYRIGHT"], [Easel copyright information])
++AC_DEFINE_UNQUOTED([EASEL_LICENSE], ["$EASEL_LICENSE"], [Easel license])
++AC_DEFINE_UNQUOTED([EASEL_VERSION], ["$EASEL_VERSION"], [Easel version])
+
+-AC_DEFINE(eslLIBRARY)
++AC_DEFINE(eslLIBRARY, [], [esl library])
+ #AC_DEFINE(hmmerLIBRARY)
+
+ # Figure out what host we're compiling on.
+@@ -182,11 +182,11 @@ AS_HELP_STRING([--enable-debugging=x],[a
+ enable_debugging=$enableval, enable_debugging=no)
+
+ case $enable_debugging in
+- yes) AC_DEFINE(eslDEBUGLEVEL, 0);;
+- 1) AC_DEFINE(eslDEBUGLEVEL, 1);;
+- 2) AC_DEFINE(eslDEBUGLEVEL, 2);;
+- 3) AC_DEFINE(eslDEBUGLEVEL, 3);;
+- no) AC_DEFINE(eslDEBUGLEVEL, 0);;
++ yes) AC_DEFINE(eslDEBUGLEVEL, 0, [no debugging]);;
++ 1) AC_DEFINE(eslDEBUGLEVEL, 1, [debug level 1]);;
++ 2) AC_DEFINE(eslDEBUGLEVEL, 2, [debug level 2]);;
++ 3) AC_DEFINE(eslDEBUGLEVEL, 3, [debug level 3]);;
++ no) AC_DEFINE(eslDEBUGLEVEL, 0, [no debugging]);;
+ *) AC_MSG_ERROR([Unknown argument to --enable-debugging: $enable_debugging]);;
+ esac
+
+@@ -293,7 +293,7 @@ case $enable_threads in
+ esac
+
+ AS_IF([test "x$check_threads" != xno],
+- [ACX_PTHREAD([AC_DEFINE(HMMER_THREADS)
++ [ACX_PTHREAD([AC_DEFINE(HMMER_THREADS, [], [Threads for hmmer])
+ AC_DEFINE(HAVE_PTHREAD)
+ AC_SUBST(PTHREAD_LIBS)
+ AC_SUBST(PTHREAD_CFLAGS)],
+@@ -356,7 +356,7 @@ AC_PROG_CC
+ AC_PROG_INSTALL
+ # MPI : set @CC@ to mpicc, sets @MPILIBS@, defines HAVE_MPI.
+ if test "$enable_mpi" = "yes"; then
+- ACX_MPI([AC_DEFINE(HAVE_MPI)
++ ACX_MPI([AC_DEFINE(HAVE_MPI, [], [MPI enabled])
+ AC_SUBST([MPI_UTESTS], ["mpi_utest"])
+ AC_SUBST([MPI_BENCHMARKS], ["mpi_benchmark"])],
+ AC_MSG_ERROR([MPI library not found for --enable-mpi]))
+@@ -376,7 +376,7 @@ CHECK_GNU_MAKE
+
+ # Select our optimization level in CFLAGS.
+ if test "$enable_debugging" != "no"; then
+- AC_DEFINE(p7_DEBUGGING, 1)
++ AC_DEFINE(p7_DEBUGGING, 1, [p7 debugging level 1])
+ if test "$GCC" = "yes" && test "$sre_cflags_env_set" = "no"; then
+ CFLAGS="-g -Wall"
+ fi
+@@ -454,7 +454,7 @@ if test "$impl_choice" = "sse"; then
+ __m128i b;
+ b = _mm_castps_si128(a);
+ a = _mm_castsi128_ps(b);]])],
+- [AC_DEFINE([HAVE_SSE2_CAST])
++ [AC_DEFINE([HAVE_SSE2_CAST], [], [compiler support for sse2 cast functions])
+ ssecast=yes])
+ AC_MSG_RESULT([$ssecast])
+ CFLAGS="$sre_save_cflags"
+@@ -531,7 +531,7 @@ if test "$impl_choice" = "sse"; then
+ [[_MM_SET_FLUSH_ZERO_MODE (_MM_FLUSH_ZERO_ON);
+ ]])],
+ [ AC_MSG_RESULT([yes])
+- AC_DEFINE([HAVE_FLUSH_ZERO_MODE])],
++ AC_DEFINE([HAVE_FLUSH_ZERO_MODE], [], [_MM_SET_FLUSH_ZERO_MODE is supported])],
+ [ AC_MSG_RESULT([no])]
+ )
+ CFLAGS="$sre_save_cflags"
+@@ -540,16 +540,16 @@ fi
+ # Now, we can enable the appropriate optimized implementation.
+ case "$impl_choice" in
+ sse) AC_MSG_NOTICE([Activating Intel/AMD SSE optimized DP implementation])
+- AC_DEFINE([HAVE_SSE2])
+- AC_DEFINE([p7_IMPL_SSE])
++ AC_DEFINE([HAVE_SSE2], [], [Activating Intel/AMD SSE optimized DP implementation])
++ AC_DEFINE([p7_IMPL_SSE], [], [Activating Intel/AMD SSE optimized DP implementation])
+ AC_SUBST([HMMERIMPLLIB], ["impl_sse/libhmmerimpl.a"])
+ IMPL_CHOICE="sse"
+ INFERNAL_IMPLDIR="impl_sse"
+ ;;
+
+ vmx) AC_MSG_NOTICE([Activating Altivec/VMX optimized DP implementation])
+- AC_DEFINE([HAVE_VMX])
+- AC_DEFINE([p7_IMPL_VMX])
++ AC_DEFINE([HAVE_VMX], [], [Activating Altivec/VMX optimized DP implementation])
++ AC_DEFINE([p7_IMPL_VMX], [], [Activating Altivec/VMX optimized DP implementation])
+ AC_SUBST([HMMERIMPLLIB], ["impl_vmx/libhmmerimpl.a"])
+ IMPL_CHOICE="vmx"
+ INFERNAL_IMPLDIR=""
+@@ -582,7 +582,7 @@ AC_PATH_PROG(HAVE_GZIP, "gzip", "no")
+ if test "${HAVE_GZIP}" = "no"; then
+ AC_MSG_WARN([gzip not found])
+ else
+- AC_DEFINE(HAVE_GZIP)
++ AC_DEFINE(HAVE_GZIP, [], [Use systm gzip library])
+ fi
+
+ # 5. Checks for libraries
=====================================
debian/patches/reproducible.patch
=====================================
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -6,7 +6,7 @@ Forwarded: https://github.com/EddyRivasLab/infernal/pull/3
Applied-Upstream: https://github.com/EddyRivasLab/infernal/commit/8cd0e3ea14e58b8bd9b60db46b73198366c87168
--- a/src/cm.c
+++ b/src/cm.c
-@@ -2854,12 +2854,17 @@
+@@ -2854,12 +2854,17 @@ cm_AppendComlog(CM_t *cm, int argc, char
int
cm_SetCtime(CM_t *cm)
{
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
#format_security.patch
reproducible.patch
+autoreconf.patch
View it on GitLab: https://salsa.debian.org/med-team/infernal/commit/a9a0482f6c228e664b9aa5a45fd2a95d8e3df029
--
View it on GitLab: https://salsa.debian.org/med-team/infernal/commit/a9a0482f6c228e664b9aa5a45fd2a95d8e3df029
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