Fix configure.ac to enable autoreconf

  * 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

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