[med-svn] [Git][med-team/hmmer2][master] Follow the hint of Andreas Metzler <ametzler at bebt.de>...
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Dec 11 15:14:38 GMT 2022
Andreas Tille pushed to branch master at Debian Med / hmmer2
Commits:
423388ac by Andreas Tille at 2022-12-11T16:13:58+01:00
Follow the hint of Andreas Metzler <ametzler at bebt.de> (https://lists.debian.org/msgid-search/Y5RiR8qidvJ4RAQt@argenau.bebt.de)
- - - - -
3 changed files:
- debian/missing-sources/configure.ac
- debian/missing-sources/get
- debian/rules
Changes:
=====================================
debian/missing-sources/configure.ac
=====================================
@@ -5,8 +5,7 @@
# Hint: See autoconf macro archive at
# http://www.gnu.org/software/ac-archive/
-# Initialize w/ AC_INIT
-AC_CONFIG_SRCDIR([<package> <version> <bug-report> <tarname>])
+# Initialize w/ AC_INIT(<package> <version> <bug-report> <tarname>)
#
# The four AC_INIT args set the following output variables and preprocessor symbols:
# PACKAGE_NAME <package> e.g. "HMMER"
@@ -25,8 +24,8 @@ AC_CONFIG_SRCDIR([<package> <version> <bug-report> <tarname>])
# The preprocessor symbols get picked up in config.h.
# The output variables are used in Makefiles.
#
-AC_PREREQ([2.71])
-AC_INIT([HMMER],[2.3.2],[eddy at genetics.wustl.edu],[hmmer])
+AC_PREREQ(2.57)
+AC_INIT(HMMER, 2.3.2, eddy at genetics.wustl.edu, hmmer)
AC_MSG_NOTICE([configuring HMMER for your system.])
PACKAGE_RELCODE="hmmer2_3_2"
@@ -109,7 +108,7 @@ AC_CANONICAL_HOST
# It sets an output variable EXEC_DEPENDENCY.
# This is used in the src/Makefile.in.
#
-AC_DEFUN([CHECK_GNU_MAKE],[
+AC_DEFUN(CHECK_GNU_MAKE,[
AC_MSG_CHECKING(whether your make is GNU make)
foundGNUmake='nope, assuming sysv make.' ;
EXEC_DEPENDENCY=[\$\$\@.o] ;
@@ -151,11 +150,11 @@ esac])
#
if test x"$enable_altivec" = xyes; then
AC_MSG_CHECKING([whether the compiler supports altivec extensions])
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[
+ AC_TRY_COMPILE([],[
#ifndef __VEC__
choke_me
#endif
- ]])],[
+ ],[
AC_MSG_RESULT([yes])
AC_MSG_NOTICE([Altivec optimization successfully enabled.])
],[
@@ -165,8 +164,8 @@ choke_me
[Either you aren't on an Apple platform that supports Altivec instructions, or your]
[compiler doesn't support Altivec. Rerun configure without the --enable-altivec]
[flag, or update to a recent compiler like gcc-3.1 (included in the latest Apple]
-[developer tools).])
- ])
+[developer tools).])]
+ )
fi
@@ -282,7 +281,7 @@ AC_SUBST(PVMLIBS)
AC_DEFUN([ACX_PTHREAD], [
AC_REQUIRE([AC_CANONICAL_HOST])
AC_LANG_SAVE
-AC_LANG([C])
+AC_LANG_C
acx_pthread_ok=no
# We used to check for pthread.h first, but this fails if pthread.h
@@ -385,9 +384,11 @@ for flag in $acx_pthread_flags; do
# pthread_cleanup_push because it is one of the few pthread
# functions on Solaris that doesn't have a non-functional libc stub.
# We try pthread_create on general principles.
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <pthread.h>]], [[pthread_t th; pthread_join(th, 0);
+ AC_TRY_LINK([#include <pthread.h>],
+ [pthread_t th; pthread_join(th, 0);
pthread_attr_init(0); pthread_cleanup_push(0, 0);
- pthread_create(0,0,0,0); pthread_cleanup_pop(0); ]])],[acx_pthread_ok=yes],[])
+ pthread_create(0,0,0,0); pthread_cleanup_pop(0); ],
+ [acx_pthread_ok=yes])
LIBS="$save_LIBS"
CFLAGS="$save_CFLAGS"
@@ -412,9 +413,13 @@ if test "x$acx_pthread_ok" = xyes; then
# Detect AIX lossage: threads are created detached by default
# and the JOINABLE attribute has a nonstandard name (UNDETACHED).
AC_MSG_CHECKING([for joinable pthread attribute])
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <pthread.h>]], [[int attr=PTHREAD_CREATE_JOINABLE;]])],[ok=PTHREAD_CREATE_JOINABLE],[ok=unknown])
+ AC_TRY_LINK([#include <pthread.h>],
+ [int attr=PTHREAD_CREATE_JOINABLE;],
+ ok=PTHREAD_CREATE_JOINABLE, ok=unknown)
if test x"$ok" = xunknown; then
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <pthread.h>]], [[int attr=PTHREAD_CREATE_UNDETACHED;]])],[ok=PTHREAD_CREATE_UNDETACHED],[ok=unknown])
+ AC_TRY_LINK([#include <pthread.h>],
+ [int attr=PTHREAD_CREATE_UNDETACHED;],
+ ok=PTHREAD_CREATE_UNDETACHED, ok=unknown)
fi
if test x"$ok" != xPTHREAD_CREATE_JOINABLE; then
AC_DEFINE(PTHREAD_CREATE_JOINABLE, $ok,
=====================================
debian/missing-sources/get
=====================================
@@ -1,3 +1,3 @@
-wget https://raw.githubusercontent.com/MichiganTech/hmmer/2.3.2/configure.ac
-cp -a configure.ac configure.ac.orig
-autoupdate
+wget https://raw.githubusercontent.com/MichiganTech/hmmer/2.3.2h2/configure.ac
+#cp -a configure.ac configure.ac.orig
+#autoupdate
=====================================
debian/rules
=====================================
@@ -9,6 +9,8 @@ endif
pkgdata:=hmmer2
sampledir:=$(CURDIR)/debian/$(pkgdata)/usr/share/doc/$(pkgdata)/examples
+export AUTOHEADER = true'
+
%:
dh $@
@@ -17,12 +19,12 @@ override_dh_clean:
rm -f configure.ac
# Trying to address #1025739 but the resulting configure file does not work
-#override_dh_autoreconf:
-# cp -a debian/missing-sources/configure.ac .
-# mv configure configure_not_used
+override_dh_autoreconf:
+ cp -a debian/missing-sources/configure.ac .
+ mv configure configure_not_used
# autoupdate
# autoreconf -f -i || true
-# dh_autoreconf
+ dh_autoreconf
override_dh_auto_configure:
dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/commit/423388accbb8c622edb663c845f1f5a6336256e1
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/commit/423388accbb8c622edb663c845f1f5a6336256e1
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