This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch debian/unstable in repository samtools.
commit 4988ce7af84ee295f63c93f3185aeea407071ade Author: Sascha Steinbiss <[email protected]> Date: Sat Jan 30 15:44:43 2016 +0000 adapt to new build system --- debian/ax_with_htslib.m4 | 140 +++++++++++++++++++++++++++++++++++++++++++++++ debian/control | 3 +- debian/patches/series | 1 - debian/rules | 21 ++++--- debian/source/options | 1 + 5 files changed, 155 insertions(+), 11 deletions(-) diff --git a/debian/ax_with_htslib.m4 b/debian/ax_with_htslib.m4 new file mode 100644 index 0000000..33831da --- /dev/null +++ b/debian/ax_with_htslib.m4 @@ -0,0 +1,140 @@ +# =========================================================================== +# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html +# =========================================================================== +# +# SYNOPSIS +# +# AX_WITH_HTSLIB +# +# DESCRIPTION +# +# This macro checks whether HTSlib <http://www.htslib.org/> is installed +# or nearby, and adds a --with-htslib=DIR option to the configure script +# for specifying the location. It locates either an installation prefix +# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as +# HTSlib is fast-moving and users may wish to use an in-development tree. +# +# Different checks occur depending on the --with-htslib argument given: +# +# With --with-htslib=DIR, checks whether DIR is a source tree or contains +# a working installation. +# By default, searches for a source tree (with a name matching htslib*) +# within or alongside $srcdir. Produces AC_MSG_ERROR if there are +# several equally-likely candidates. If there are none, checks for +# a working default installation. +# With --with-htslib=system, checks for a working default installation. +# +# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS +# (which unfortunately may cause a "you should use literals" warning when +# autoconf is run). +# +# The following output variables are set by this macro: +# +# HTSDIR Directory containing HTSlib source tree +# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib +# HTSLIB_LDFLAGS Linker flags for linking with HTSlib +# +# The following shell variables may be defined: +# +# ax_cv_htslib Set to "yes" if HTSlib was found +# ax_cv_htslib_which Set to "source", "install", or "none" +# +# LICENSE +# +# Copyright (C) 2015 Genome Research Ltd +# +# Copying and distribution of this file, with or without modification, are +# permitted in any medium without royalty provided the copyright notice +# and this notice are preserved. This file is offered as-is, without any +# warranty. + +#serial 1 + +AC_DEFUN([AX_WITH_HTSLIB], +[AC_ARG_WITH([htslib], + [AS_HELP_STRING([--with-htslib=DIR], + [use the HTSlib source tree or installation in DIR]) +dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() +AS_HELP_STRING([--with-htslib=system], + [use only a system HTSlib installation])], + [], [with_htslib=search]) + +case $with_htslib in +yes|search) + AC_MSG_CHECKING([location of HTSlib source tree]) + case $srcdir in + .) srcp= ;; + *) srcp=$srcdir/ ;; + esac + found= + for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* + do + if test "$dir" = "--"; then + test -n "$found" && break + elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then + found="${found}1" + HTSDIR=$dir + fi + done + if test -z "$found"; then + AC_MSG_RESULT([none found]) + ax_cv_htslib_which=system + elif test "$found" = 1; then + AC_MSG_RESULT([$HTSDIR]) + ax_cv_htslib_which=source + else + AC_MSG_RESULT([several directories found]) + AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) + fi + ;; +no) ax_cv_htslib_which=none ;; +system) ax_cv_htslib_which=system ;; +*) + HTSDIR=$with_htslib + if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then + ax_cv_htslib_which=source + else + ax_cv_htslib_which=install + fi + ;; +esac + +case $ax_cv_htslib_which in +source) + ax_cv_htslib=yes + HTSLIB_CPPFLAGS="-I$HTSDIR" + HTSLIB_LDFLAGS="-L$HTSDIR" + # We can't use a literal, because $HTSDIR is user-provided and variable + AC_CONFIG_SUBDIRS($HTSDIR) + ;; +system) + AC_CHECK_HEADER([htslib/sam.h], + [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], + [ax_cv_htslib=no], [;]) + ax_cv_htslib_which=install + HTSDIR= + HTSLIB_CPPFLAGS= + HTSLIB_LDFLAGS= + ;; +install) + ax_saved_CPPFLAGS=$CPPFLAGS + ax_saved_LDFLAGS=$LDFLAGS + HTSLIB_CPPFLAGS="-I$HTSDIR/include" + HTSLIB_LDFLAGS="-L$HTSDIR/lib" + CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" + LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" + AC_CHECK_HEADER([htslib/sam.h], + [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], + [ax_cv_htslib=no], [;]) + HTSDIR= + CPPFLAGS=$ax_saved_CPPFLAGS + LDFLAGS=$ax_saved_LDFLAGS + ;; +none) + ax_cv_htslib=no + ;; +esac + +AC_SUBST([HTSDIR]) +AC_SUBST([HTSLIB_CPPFLAGS]) +AC_SUBST([HTSLIB_LDFLAGS])]) diff --git a/debian/control b/debian/control index 9afef7e..74f6b44 100644 --- a/debian/control +++ b/debian/control @@ -9,8 +9,9 @@ Build-Depends: debhelper (>= 9), # libio-pty-perl is needed by the regression test. libio-pty-perl, libncurses5-dev, - libhts-dev (>= 1.2), + libhts-dev (>= 1.3), zlib1g-dev, + autoconf-archive, tabix (>= 1.0) # tabix is needed for the regression tests. Standards-Version: 3.9.6 diff --git a/debian/patches/series b/debian/patches/series index 3347f33..83bdf44 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1 @@ -dynamic-build.patch mayhem.patch diff --git a/debian/rules b/debian/rules index 4586a09..d6aae77 100755 --- a/debian/rules +++ b/debian/rules @@ -5,24 +5,27 @@ export DH_VERBOSE=1 %: dh $@ --parallel +override_dh_auto_clean: + touch config.mk + dh_auto_clean -- + +override_dh_auto_configure: + touch config.mk + aclocal --force -I /usr/share/aclocal/ -I debian/ + autoconf + dh_auto_configure -- --with-htslib=system + override_dh_auto_build: dh_auto_build -- \ - HTSDIR="/usr/include" \ - HTSLIB=$(shell dpkg -S libhts.a | awk '{print $$2}') \ CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$$(DFLAGS) \$$(INCLUDES) $$(dpkg-buildflags --get CPPFLAGS)" \ - LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \ - LIBS="-lhts" + LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" override_dh_auto_test: dh_auto_test -- \ - HTSDIR="/usr/include" \ - HTSLIB=$(shell dpkg -S libhts.a | awk '{print $$2}') \ BGZIP=/usr/bin/bgzip override_dh_auto_install: dh_auto_install -- \ - prefix=/usr \ - HTSDIR="/usr/include" \ - HTSLIB=$(shell dpkg -S libhts.a | awk '{print $$2}') + prefix=/usr make clean diff --git a/debian/source/options b/debian/source/options index 7423a2d..ae4cafe 100644 --- a/debian/source/options +++ b/debian/source/options @@ -1 +1,2 @@ single-debian-patch +extend-diff-ignore = "^(\.travis.*|README.md)$" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
