[med-svn] [Git][med-team/hmmer2][master] 5 commits: Fix build with configure.ac
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Dec 11 16:03:56 GMT 2022
Andreas Tille pushed to branch master at Debian Med / hmmer2
Commits:
f3fe7a54 by Andreas Tille at 2022-12-11T16:57:13+01:00
Fix build with configure.ac
- - - - -
12697ef7 by Andreas Tille at 2022-12-11T16:57:43+01:00
Fix watchfile to detect new versions on github
- - - - -
0522007a by Andreas Tille at 2022-12-11T16:57:45+01:00
routine-update: Standards-Version: 4.6.1
- - - - -
2e4ba4c7 by Andreas Tille at 2022-12-11T16:58:17+01:00
Apply multi-arch hints.
+ hmmer2-doc: Add Multi-Arch: foreign.
+ libhmmer2-dev: Add Multi-Arch: same.
Changes-By: apply-multiarch-hints
- - - - -
fd3eb0a0 by Andreas Tille at 2022-12-11T16:59:13+01:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- − debian/missing-sources/configure.ac.orig
- debian/missing-sources/get
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,11 @@
-hmmer2 (2.3.2+dfsg-8) UNRELEASED; urgency=medium
+hmmer2 (2.3.2+dfsg-8) unstable; urgency=medium
* Provide configure.ac as source for configure
Closes: #1025739
+ * Fix watchfile to detect new versions on github
+ * Standards-Version: 4.6.1 (routine-update)
- -- Andreas Tille <tille at debian.org> Fri, 09 Dec 2022 16:20:24 +0100
+ -- Andreas Tille <tille at debian.org> Sun, 11 Dec 2022 16:58:23 +0100
hmmer2 (2.3.2+dfsg-7) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13),
pkg-config,
dh-exec,
rename
-Standards-Version: 4.5.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/hmmer2
Vcs-Git: https://salsa.debian.org/med-team/hmmer2.git
Homepage: http://hmmer.janelia.org/
@@ -39,6 +39,7 @@ Depends: ${shlibs:Depends},
${misc:Depends}
Recommends: hmmer2 (>= ${source:Version}),
xpdf-reader | pdf-viewer
+Multi-Arch: foreign
Description: profile hidden Markov models for protein sequence analysis (docs)
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
@@ -56,6 +57,7 @@ Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends}
+Multi-Arch: same
Description: profile hidden Markov models for protein sequence analysis (devel)
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
=====================================
debian/missing-sources/configure.ac.orig deleted
=====================================
@@ -1,538 +0,0 @@
-# Process this file with autoconf to produce a configure script.
-# SRE, Mon Oct 5 14:55:45 1998
-# CVS $Id$
-#
-# Hint: See autoconf macro archive at
-# http://www.gnu.org/software/ac-archive/
-
-# 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"
-# PACKAGE_VERSION <version> e.g. "2.2h"
-# PACKAGE_BUGREPORT <bug-report> e.g. "eddy at genetics.wustl.edu"
-# PACKAGE_TARNAME <tarname> e.g. "hmmer"
-# From them, it derives one more:
-# PACKAGE_STRING <package> <version>, e.g. "HMMER 2.2h"
-# We also define additional variables:
-# PACKAGE_RELCODE unique CVS tag without .'s: e.g. "hmmer2_2i"
-# PACKAGE_DATE release date: e.g. "January 2003"
-# PACKAGE_COPYRIGHT one-line copyright string
-# PACKAGE_LICENSE one-line license string
-# PACKAGE_LICENSETAG which license to bundle from Licenses/ subdirectory.
-#
-# The preprocessor symbols get picked up in config.h.
-# The output variables are used in Makefiles.
-#
-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"
-PACKAGE_DATE="Oct 2003"
-PACKAGE_COPYRIGHT="Copyright (C) 1992-2003 HHMI/Washington University School of Medicine"
-PACKAGE_LICENSE="Freely distributed under the GNU General Public License (GPL)"
-PACKAGE_LICENSETAG=gnu
-
-
-
-
-# For a normal release, you don't need to edit below this line.
-#
-AC_SUBST(PACKAGE_RELCODE)
-AC_SUBST(PACKAGE_DATE)
-AC_SUBST(PACKAGE_COPYRIGHT)
-AC_SUBST(PACKAGE_LICENSE)
-AC_SUBST(PACKAGE_LICENSETAG)
-
-AC_DEFINE_UNQUOTED(PACKAGE_DATE, "$PACKAGE_DATE")
-AC_DEFINE_UNQUOTED(PACKAGE_COPYRIGHT, "$PACKAGE_COPYRIGHT")
-AC_DEFINE_UNQUOTED(PACKAGE_LICENSE, "$PACKAGE_LICENSE")
-
-
-# Check if we're a binary distribution.
-# The trigger for this is the existence of the binaries/ subdirectory,
-# and the nonexistence of a src/ subdirectory.
-#
-# If we are a binary dist, we only do a minimal configuration, setting up
-# version information and installation path names.
-# This makes ./configure independent of having a working
-# C compiler.
-#
-# Watch out: this is implemented as a sneaky if statement that wraps the
-# majority of the configure.ac M4 code.
-#
-if ((! test -d binaries) && test -d src); then
-AC_MSG_NOTICE([This is a full source distribution - using full config])
-
-# Checks for programs.
-# Sets output variables CC, CFLAGS, and RANLIB.
-# AR might be hidden away on Solaris; provide some hints in the PATH.
-#
-AC_PROG_CC
-AC_PROG_RANLIB
-AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
-
-
-# Figure out what host we're compiling on.
-# Three GNU scripts must be included in the distro:
-# install.sh, config.guess, config.sub
-# This sets four shell variables:
-# host example: i686-pc-linux-gnu
-# host_cpu example: i686
-# host_vendor example: pc
-# host_os example: linux-gnu
-#
-# These are used later in the configure by the ACX_PTHREAD macro to determine
-# system-specific details of threads libraries.
-#
-AC_CANONICAL_HOST
-
-
-
-# GNU make check; format of makefile dependency lines for executables.
-# original from John Darrington <j.darrington at elvis.murdoch.edu.au>
-# w/ heavy modifications.
-#
-# We need this because GNU make and SYSV make use different systems
-# specifying variables for dependencies: $$@ in sysv, %: %.o in GNU.
-# Would love to hear a better way of doing this.
-#
-# I use two different conventions in my Makefiles. Sometimes
-# executable "foo" has a file "foo.c" - this is the HMMER convention.
-# Sometimes executable "foo" has a file "foo_main.c" - this is
-# the SQUID convention. The configure script sets the
-# EXEC_DEPENDENCY appropriately: here, HMMER style.
-#
-# This creates a function CHECK_GNU_MAKE, which we immediately call.
-# It sets an output variable EXEC_DEPENDENCY.
-# This is used in the src/Makefile.in.
-#
-AC_DEFUN(CHECK_GNU_MAKE,[
- AC_MSG_CHECKING(whether your make is GNU make)
- foundGNUmake='nope, assuming sysv make.' ;
- EXEC_DEPENDENCY=[\$\$\@.o] ;
- if ( make --version nothing 2> /dev/null | grep GNU > /dev/null ) ; then
- foundGNUmake='yes, it is.' ;
- EXEC_DEPENDENCY='%: %.o' ;
- fi
- AC_MSG_RESULT($foundGNUmake)
- AC_SUBST(EXEC_DEPENDENCY)
-])
-CHECK_GNU_MAKE
-
-#################################################################################
-# Now we're into our "optional features"
-#################################################################################
-
-
-# --enable-altivec - enable Erik Lindahl's Altivec code for PowerPC
-#
-# Sets the ALTIVEC preprocessor variable; adds -faltivec to the CFLAGS.
-#
-AC_ARG_ENABLE(altivec,
-[ --enable-altivec enable Altivec-specific code for PowerPC],
-[case $enable_altivec in
- yes) AC_MSG_NOTICE([enabled Altivec optimization for PowerPC (Erik Lindahl)])
- AC_DEFINE(ALTIVEC)
- CFLAGS="$CFLAGS -faltivec"
- ;;
- no) AC_MSG_NOTICE([Altivec/PowerPC optimization disabled])
- ;;
- *) echo "Ignoring unknown argument to --enable-altivec: $enable_altivec"
- ;;
-esac])
-#
-# Now check whether the compiler supports altivec extensions, if enabled..
-# In theory we could do this in the source, but this way we can give
-# the user an explicit error message telling him/her to upgrade the compiler.
-# (M4 code from Erik Lindahl, Stanford University)
-#
-if test x"$enable_altivec" = xyes; then
- AC_MSG_CHECKING([whether the compiler supports altivec extensions])
- AC_TRY_COMPILE([],[
-#ifndef __VEC__
-choke_me
-#endif
- ],[
- AC_MSG_RESULT([yes])
- AC_MSG_NOTICE([Altivec optimization successfully enabled.])
- ],[
- AC_MSG_RESULT([no])
- AC_MSG_ERROR([altivec not supported on this platform]
-[]
-[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).])]
- )
-fi
-
-
-
-# --enable-ccmalloc - configure for compiling in ccmalloc memory checks
-#
-# The CC output variable is modified.
-# Requires ccmalloc version >= 0.4.0 because of the --no-wrapper option.
-#
-AC_ARG_ENABLE(ccmalloc,
-[ --enable-ccmalloc turn ccmalloc memory debugging on ],
-[case $enable_ccmalloc in
- yes) AC_MSG_NOTICE([enabled ccmalloc memory debugging])
- CC="ccmalloc --no-wrapper $CC"
- ;;
- no) AC_MSG_NOTICE([ccmalloc memory debug/tracing disabled])
- ;;
- *) echo "Ignoring unknown argument to --enable-ccmalloc: $enable_ccmalloc"
- ;;
-esac])
-
-
-# --enable-debugging=x - set debugging level to <x> (1-3)
-#
-# At all levels, including 0, replaces CFLAGS w/ "-g -Wall" (so it assumes gcc).
-# Sets the DEBUGLEVEL preprocessor symbol to <x>
-#
-AC_ARG_ENABLE(debugging,
-[ --enable-debugging set CFLAGS for debugging
- --enable-debugging=x also set diagnostics level to <x> (1-3)
- (where 3 = most verbose)],
-[ case $enable_debugging in
- yes) AC_MSG_NOTICE([enabled debugging diagnostics level 0 (CFLAGS only, no verbosity)])
- CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 0)
- ;;
- 1) AC_MSG_NOTICE([enabled debugging diagnostics level 1 (low verbosity)])
- CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 1)
- ;;
- 2) AC_MSG_NOTICE([enabled debugging diagnostics level 2 (moderate verbosity)])
- CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 2)
- ;;
- 3) AC_MSG_NOTICE([enabled debugging diagnostics level 3 (high verbosity)])
- CFLAGS="-g -Wall"
- AC_DEFINE(DEBUGLEVEL, 3)
- ;;
- no) AC_MSG_NOTICE([debugging diagnostics disabled])
- ;;
- *) echo "Ignoring unknown argument to --enable-debugging: $enable_debugging"
- ;;
-esac])
-
-
-# --enable-lfs Large File Summit (LFS) support for >2GB files
-# See: http://ftp.sas.com/standards/large.file/x_open.20Mar96.html
-#
-AC_ARG_ENABLE(lfs,
-[ --enable-lfs enable LFS, Large File Support],
-[case $enable_lfs in
- yes) AC_MSG_NOTICE([configured for optional LFS, large file support])
- AC_DEFINE(_LARGEFILE_SOURCE)
- AC_DEFINE(_LARGEFILE64_SOURCE)
- AC_DEFINE(_FILE_OFFSET_BITS, 64)
- ;;
- no) ;;
- *) echo "Ignoring unknown argument to --enable-lfs: $enable_lfs"
- ;;
-esac])
-
-
-
-# --enable-pvm Enable Parallel Virtual Machine (PVM) support
-#
-# Sets PVMLIBDIR, PVMINCDIR, PCMPROGS, PVMLIBS output variables
-# Sets HMMER_PVM preprocessor variable.
-#
-AC_ARG_ENABLE(pvm,
-[ --enable-pvm enable PVM, Parallel Virtual Machine],
-[case $enable_pvm in
- yes) AC_MSG_NOTICE([enabled optional PVM (Parallel Virtual Machine) support])
- PVMLIBDIR="-L${PVM_ROOT}/lib/${PVM_ARCH}"
- PVMINCDIR="-I${PVM_ROOT}/include"
- PVMPROGS="hmmcalibrate-pvm hmmpfam-pvm hmmsearch-pvm"
- PVMLIBS="-lpvm3"
- AC_DEFINE(HMMER_PVM)
- ;;
- no) AC_MSG_NOTICE([PVM (Parallel Virtual machine) support disabled])
- ;;
- *) echo "Ignoring unknown argument to --enable-pvm: $enable_pvm"
- ;;
-esac])
-AC_SUBST(PVMLIBDIR)
-AC_SUBST(PVMINCDIR)
-AC_SUBST(PVMPROGS)
-AC_SUBST(PVMLIBS)
-
-
-# --enable-threads Enable POSIX multithreading
-#
-# Uses ACX_PTHREAD macro from the GNU macro archive.
-# ****************************************************************
-# ****************************************************************
-#
-# The ACX_PTHREAD macro.
-# Synopsis: ACX_PTHREAD([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
-# Authors: Steven G. Johnson <stevenj at alum.mit.edu>
-# Alejandro Forero Cuervo <bachue at bachue.com>
-# Version: 1.8 (2003/05/21)
-# Source: http://www.gnu.org/software/ac-archive/htmldoc/acx_pthread.html
-#
-AC_DEFUN([ACX_PTHREAD], [
-AC_REQUIRE([AC_CANONICAL_HOST])
-AC_LANG_SAVE
-AC_LANG_C
-acx_pthread_ok=no
-
-# We used to check for pthread.h first, but this fails if pthread.h
-# requires special compiler flags (e.g. on True64 or Sequent).
-# It gets checked for in the link test anyway.
-
-# First of all, check if the user has set any of the PTHREAD_LIBS,
-# etcetera environment variables, and if threads linking works using
-# them:
-if test x"$PTHREAD_LIBS$PTHREAD_CFLAGS" != x; then
- save_CFLAGS="$CFLAGS"
- CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
- save_LIBS="$LIBS"
- LIBS="$PTHREAD_LIBS $LIBS"
- AC_MSG_CHECKING([for pthread_join in LIBS=$PTHREAD_LIBS with CFLAGS=$PTHREAD_CFLAGS])
- AC_TRY_LINK_FUNC(pthread_join, acx_pthread_ok=yes)
- AC_MSG_RESULT($acx_pthread_ok)
- if test x"$acx_pthread_ok" = xno; then
- PTHREAD_LIBS=""
- PTHREAD_CFLAGS=""
- fi
- LIBS="$save_LIBS"
- CFLAGS="$save_CFLAGS"
-fi
-
-# We must check for the threads library under a number of different
-# names; the ordering is very important because some systems
-# (e.g. DEC) have both -lpthread and -lpthreads, where one of the
-# libraries is broken (non-POSIX).
-
-# Create a list of thread flags to try. Items starting with a "-" are
-# C compiler flags, and other items are library names, except for "none"
-# which indicates that we try without any flags at all.
-
-acx_pthread_flags="pthreads none -Kthread -kthread lthread -pthread -pthreads -mthreads pthread --thread-safe -mt"
-
-# The ordering *is* (sometimes) important. Some notes on the
-# individual items follow:
-
-# pthreads: AIX (must check this before -lpthread)
-# none: in case threads are in libc; should be tried before -Kthread and
-# other compiler flags to prevent continual compiler warnings
-# -Kthread: Sequent (threads in libc, but -Kthread needed for pthread.h)
-# -kthread: FreeBSD kernel threads (preferred to -pthread since SMP-able)
-# lthread: LinuxThreads port on FreeBSD (also preferred to -pthread)
-# -pthread: Linux/gcc (kernel threads), BSD/gcc (userland threads)
-# -pthreads: Solaris/gcc
-# -mthreads: Mingw32/gcc, Lynx/gcc
-# -mt: Sun Workshop C (may only link SunOS threads [-lthread], but it
-# doesn't hurt to check since this sometimes defines pthreads too;
-# also defines -D_REENTRANT)
-# pthread: Linux, etcetera
-# --thread-safe: KAI C++
-
-case "${host_cpu}-${host_os}" in
- *solaris*)
-
- # On Solaris (at least, for some versions), libc contains stubbed
- # (non-functional) versions of the pthreads routines, so link-based
- # tests will erroneously succeed. (We need to link with -pthread or
- # -lpthread.) (The stubs are missing pthread_cleanup_push, or rather
- # a function called by this macro, so we could check for that, but
- # who knows whether they'll stub that too in a future libc.) So,
- # we'll just look for -pthreads and -lpthread first:
-
- acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
- ;;
-esac
-
-if test x"$acx_pthread_ok" = xno; then
-for flag in $acx_pthread_flags; do
-
- case $flag in
- none)
- AC_MSG_CHECKING([whether pthreads work without any flags])
- ;;
-
- -*)
- AC_MSG_CHECKING([whether pthreads work with $flag])
- PTHREAD_CFLAGS="$flag"
- ;;
-
- *)
- AC_MSG_CHECKING([for the pthreads library -l$flag])
- PTHREAD_LIBS="-l$flag"
- ;;
- esac
-
- save_LIBS="$LIBS"
- save_CFLAGS="$CFLAGS"
- LIBS="$PTHREAD_LIBS $LIBS"
- CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
-
- # Check for various functions. We must include pthread.h,
- # since some functions may be macros. (On the Sequent, we
- # need a special flag -Kthread to make this header compile.)
- # We check for pthread_join because it is in -lpthread on IRIX
- # while pthread_create is in libc. We check for pthread_attr_init
- # due to DEC craziness with -lpthreads. We check for
- # pthread_cleanup_push because it is one of the few pthread
- # functions on Solaris that doesn't have a non-functional libc stub.
- # We try pthread_create on general principles.
- AC_TRY_LINK([#include <pthread.h>],
- [pthread_t th; pthread_join(th, 0);
- pthread_attr_init(0); pthread_cleanup_push(0, 0);
- pthread_create(0,0,0,0); pthread_cleanup_pop(0); ],
- [acx_pthread_ok=yes])
-
- LIBS="$save_LIBS"
- CFLAGS="$save_CFLAGS"
-
- AC_MSG_RESULT($acx_pthread_ok)
- if test "x$acx_pthread_ok" = xyes; then
- break;
- fi
-
- PTHREAD_LIBS=""
- PTHREAD_CFLAGS=""
-done
-fi
-
-# Various other checks:
-if test "x$acx_pthread_ok" = xyes; then
- save_LIBS="$LIBS"
- LIBS="$PTHREAD_LIBS $LIBS"
- save_CFLAGS="$CFLAGS"
- CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
-
- # Detect AIX lossage: threads are created detached by default
- # and the JOINABLE attribute has a nonstandard name (UNDETACHED)..
- AC_MSG_CHECKING([for joinable pthread attribute])
- AC_TRY_LINK([#include <pthread.h>],
- [int attr=PTHREAD_CREATE_JOINABLE;],
- ok=PTHREAD_CREATE_JOINABLE, ok=unknown)
- if test x"$ok" = xunknown; then
- 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, $ok,
- [Define to the necessary symbol if this constant
- uses a non-standard name on your system.])
- fi
- AC_MSG_RESULT(${ok})
- if test x"$ok" = xunknown; then
- AC_MSG_WARN([we do not know how to create joinable pthreads])
- fi
-
- AC_MSG_CHECKING([if more special flags are required for pthreads])
- flag=no
- case "${host_cpu}-${host_os}" in
- *-aix* | *-freebsd*) flag="-D_THREAD_SAFE";;
- *solaris* | *-osf* | *-hpux*) flag="-D_REENTRANT";;
- esac
- AC_MSG_RESULT(${flag})
- if test "x$flag" != xno; then
- PTHREAD_CFLAGS="$flag $PTHREAD_CFLAGS"
- fi
-
- LIBS="$save_LIBS"
- CFLAGS="$save_CFLAGS"
-
- # More AIX lossage: must compile with cc_r
- AC_CHECK_PROG(PTHREAD_CC, cc_r, cc_r, ${CC})
-else
- PTHREAD_CC="$CC"
-fi
-
-AC_SUBST(PTHREAD_LIBS)
-AC_SUBST(PTHREAD_CFLAGS)
-AC_SUBST(PTHREAD_CC)
-
-# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
-if test x"$acx_pthread_ok" = xyes; then
- ifelse([$1],,AC_DEFINE(HAVE_PTHREAD,1,[Define if you have POSIX threads libraries and header files.]),[$1])
- :
-else
- acx_pthread_ok=no
- $2
-fi
-AC_LANG_RESTORE
-])dnl ACX_PTHREAD
-# ACX_PTHREAD macro end.
-# ****************************************************************
-# ****************************************************************
-
-#
-# Back to my code to finish enabling pthreads...
-# Define these preprocessor variables:
-# HMMER_THREADS
-# HAVE_PTHREAD_SETCONCURRENCY
-# HAVE_PTHREAD_ATTR_SETSCOPE
-#
-AC_ARG_ENABLE(threads,
-[ --enable-threads enable POSIX multithreading support],
-[case $enable_threads in
- yes) AC_MSG_NOTICE([enabled POSIX multithreading support])
- AC_CHECK_FUNCS(pthread_setconcurrency)
- AC_CHECK_FUNCS(pthread_attr_setscope)
- ACX_PTHREAD(AC_DEFINE(HMMER_THREADS))
- ;;
- no) AC_MSG_NOTICE([POSIX multithreading support disabled])
- ;;
- *) echo "Ignoring unknown argument to --disable-threads: $enable_threads"
- ;;
-esac])
-
-
-# Check for incompatible optional features
-#
-if test x"$enable_threads" = xyes; then
- if test x"$enable_ccmalloc" = xyes; then
- AC_MSG_ERROR([ccmalloc probably not threadsafe; do not enable both ccmalloc and threads])
- fi
-fi
-
-
-# Although we configure our fixed-size integers in squid,
-# we do need some of that configuration code here, because
-# we might (on Solaris, for instance) need to include
-# -lsocket to the linker to get ntohs() and friends. These
-# define preprocessor variables HAVE_NTOHS, HAVE_NTOHL,
-# HAVE_HTONS, and HAVE_HTONL.
-#
-AC_CHECK_FUNCS(ntohs, , AC_CHECK_LIB(socket, ntohs))
-AC_CHECK_FUNCS(ntohl, , AC_CHECK_LIB(socket, ntohl))
-AC_CHECK_FUNCS(htons, , AC_CHECK_LIB(socket, htons))
-AC_CHECK_FUNCS(htonl, , AC_CHECK_LIB(socket, htonl))
-
-# Configure the squid library
-#
-AC_CONFIG_SUBDIRS(squid)
-
-# Write the config.h header
-#
-AC_CONFIG_HEADERS(src/config.h)
-
-# Write out Makefiles
-#
-AC_CONFIG_FILES(src/Makefile)
-AC_CONFIG_FILES(testsuite/Makefile)
-
-# remember that sneaky if statement that wraps the source
-# configuration? well, it ends here.
-else
- AC_MSG_NOTICE([This is a precompiled binary distribution - using abbreviated config])
-fi
-
-AC_CONFIG_FILES(Makefile)
-AC_OUTPUT
-
-
-
=====================================
debian/missing-sources/get
=====================================
@@ -1,3 +1,7 @@
+#!/bin/sh
+# Thanks to Andreas Metzler <ametzler at bebt.de> (https://lists.debian.org/msgid-search/Y5RiR8qidvJ4RAQt@argenau.bebt.de)
+# and Boyuan Yang <byang at debian.org>
+
wget https://raw.githubusercontent.com/MichiganTech/hmmer/2.3.2h2/configure.ac
#cp -a configure.ac configure.ac.orig
#autoupdate
=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ endif
pkgdata:=hmmer2
sampledir:=$(CURDIR)/debian/$(pkgdata)/usr/share/doc/$(pkgdata)/examples
-export AUTOHEADER = true'
+export AUTOHEADER = 'true'
%:
dh $@
=====================================
debian/watch
=====================================
@@ -17,4 +17,4 @@ opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
# There is some effort to continue hmmer2 but see the discussion here
# https://alioth-lists.debian.net/pipermail/debian-med-packaging/2020-August/083899.html
#opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-# https://github.com/MichiganTech/hmmer/releases .*/archive/(2\..*)@ARCHIVE_EXT@
+# https://github.com/MichiganTech/hmmer/releases .*/(2\..*)@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/423388accbb8c622edb663c845f1f5a6336256e1...fd3eb0a0d832a592bb9521d51a3da9b1f9dd6f19
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/423388accbb8c622edb663c845f1f5a6336256e1...fd3eb0a0d832a592bb9521d51a3da9b1f9dd6f19
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