Commit a9a0482f authored by Andreas Tille's avatar Andreas Tille

Fix configure.ac to enable autoreconf

parent cd5470b8
......@@ -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@debian.org> Wed, 18 Jan 2017 12:56:58 +0100
......
Author: Andreas Tille <tille@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
......@@ -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)
{
......
#format_security.patch
reproducible.patch
autoreconf.patch
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment