[med-svn] [Git][med-team/hmmer2][master] 2 commits: Provide configure.ac as source for configure
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Dec 9 16:32:03 GMT 2022
Andreas Tille pushed to branch master at Debian Med / hmmer2
Commits:
5f816b20 by Andreas Tille at 2022-12-09T16:59:57+01:00
Provide configure.ac as source for configure
- - - - -
d1f5b3d0 by Andreas Tille at 2022-12-09T17:30:33+01:00
Trying to address #1025739 but the resulting configure file does not work
- - - - -
5 changed files:
- debian/changelog
- + debian/missing-sources/configure.ac
- + debian/missing-sources/configure.ac.orig
- + debian/missing-sources/get
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+hmmer2 (2.3.2+dfsg-8) UNRELEASED; urgency=medium
+
+ * Provide configure.ac as source for configure
+ Closes: #1025739
+
+ -- Andreas Tille <tille at debian.org> Fri, 09 Dec 2022 16:20:24 +0100
+
hmmer2 (2.3.2+dfsg-7) unstable; urgency=medium
* Drop hmmer2-pvm package
=====================================
debian/missing-sources/configure.ac
=====================================
@@ -0,0 +1,533 @@
+# 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
+AC_CONFIG_SRCDIR([<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([2.71])
+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_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[
+#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_LINK_IFELSE([AC_LANG_PROGRAM([[#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_LINK_IFELSE([AC_LANG_PROGRAM([[#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])
+ 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/configure.ac.orig
=====================================
@@ -0,0 +1,538 @@
+# 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"$enable_ccmalloc" = xyes; then
+ AC_MSG_ERROR([ccmalloc probably not threadsafe; do not enable both ccmalloc and threads])
+ fi
+fi
+
+
+# Although we configure our fixed-size integers in squid,
+# we do need some of that configuration code here, because
+# we might (on Solaris, for instance) need to include
+# -lsocket to the linker to get ntohs() and friends. These
+# define preprocessor variables HAVE_NTOHS, HAVE_NTOHL,
+# HAVE_HTONS, and HAVE_HTONL.
+#
+AC_CHECK_FUNCS(ntohs, , AC_CHECK_LIB(socket, ntohs))
+AC_CHECK_FUNCS(ntohl, , AC_CHECK_LIB(socket, ntohl))
+AC_CHECK_FUNCS(htons, , AC_CHECK_LIB(socket, htons))
+AC_CHECK_FUNCS(htonl, , AC_CHECK_LIB(socket, htonl))
+
+# Configure the squid library
+#
+AC_CONFIG_SUBDIRS(squid)
+
+# Write the config.h header
+#
+AC_CONFIG_HEADERS(src/config.h)
+
+# Write out Makefiles
+#
+AC_CONFIG_FILES(src/Makefile)
+AC_CONFIG_FILES(testsuite/Makefile)
+
+# remember that sneaky if statement that wraps the source
+# configuration? well, it ends here.
+else
+ AC_MSG_NOTICE([This is a precompiled binary distribution - using abbreviated config])
+fi
+
+AC_CONFIG_FILES(Makefile)
+AC_OUTPUT
+
+
+
=====================================
debian/missing-sources/get
=====================================
@@ -0,0 +1,3 @@
+wget https://raw.githubusercontent.com/MichiganTech/hmmer/2.3.2/configure.ac
+cp -a configure.ac configure.ac.orig
+autoupdate
=====================================
debian/rules
=====================================
@@ -12,6 +12,18 @@ sampledir:=$(CURDIR)/debian/$(pkgdata)/usr/share/doc/$(pkgdata)/examples
%:
dh $@
+override_dh_clean:
+ if [ -e configure_not_used ] ; then mv configure_not_used configure; fi
+ 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
+# autoupdate
+# autoreconf -f -i || true
+# dh_autoreconf
+
override_dh_auto_configure:
dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm
# avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together)
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/029fa062a55b25ead843c5f530febcdf5ed40b89...d1f5b3d08391efd66b69090e544803d6bd0f6638
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/029fa062a55b25ead843c5f530febcdf5ed40b89...d1f5b3d08391efd66b69090e544803d6bd0f6638
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