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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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