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 <[email protected]> (https://lists.debian.org/msgid-search/[email protected]) - - - - - 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],[[email protected]],[hmmer]) +AC_PREREQ(2.57) +AC_INIT(HMMER, 2.3.2, [email protected], 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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
