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commit 0206c3d81e695291f17b780e77e671f95e36860b Author: Afif Elghraoui <a...@debian.org> Date: Mon Aug 7 20:09:34 2017 -0400 Update packaging for new build system --- debian/control | 3 ++- debian/patches/destdir.patch | 26 -------------------------- debian/patches/fix_config.mk.patch | 11 ----------- debian/patches/series | 1 - debian/rules | 27 ++++++++++++++++++--------- 5 files changed, 20 insertions(+), 48 deletions(-) diff --git a/debian/control b/debian/control index 3423f5d..8fc52e2 100644 --- a/debian/control +++ b/debian/control @@ -6,8 +6,9 @@ Uploaders: Afif Elghraoui <a...@debian.org> Build-Depends: debhelper (>= 10), - autoconf-archive, zlib1g-dev, + libbz2-dev, + liblzma-dev, libhts-dev (>= 1.5), libgsl-dev, # Test-Depends: diff --git a/debian/patches/destdir.patch b/debian/patches/destdir.patch deleted file mode 100644 index b3bb456..0000000 --- a/debian/patches/destdir.patch +++ /dev/null @@ -1,26 +0,0 @@ -Description: Set installation prefix -Author: Afif Elghraoui <a...@ghraoui.name> -Forwarded: not-needed -Last-Update: 2015-11-03 ---- a/Makefile -+++ b/Makefile -@@ -41,7 +41,7 @@ OBJS = main.o vcfindex.o tabix.o \ - mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \ - ccall.o em.o prob1.o kmin.o # the original samtools calling - --prefix = /usr/local -+prefix = /usr - exec_prefix = $(prefix) - bindir = $(exec_prefix)/bin - libdir = $(exec_prefix)/lib ---- a/config.mk.in -+++ b/config.mk.in -@@ -47,7 +47,7 @@ GSL_LIBS = -lgsl -lgslcblas - - PLATFORM = @PLATFORM@ - PLUGINS_ENABLED = @enable_bcftools_plugins@ --plugindir = @bcf_plugindir@ -+plugindir ?= @bcf_plugindir@ - PLUGIN_EXT = @PLUGIN_EXT@ - - @Hsource@BGZIP = /usr/bin/bgzip diff --git a/debian/patches/fix_config.mk.patch b/debian/patches/fix_config.mk.patch deleted file mode 100644 index 3f80c2c..0000000 --- a/debian/patches/fix_config.mk.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/Makefile -+++ b/Makefile -@@ -81,7 +81,7 @@ ALL_LIBS = -lz -ldl $(LIBS) - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. - config.mk: -- @sed -e '/^prefix/,/^PLUGIN_EXT/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#../htslib#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;' config.mk.in > $@ -+ @sed -e '/^prefix/,/^PLUGIN_EXT/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#/usr/lib/htslib#g;s#@HTSLIB_CPPFLAGS@#-I/usr/include#g;' config.mk.in > $@ - - config.h: - echo '/* Basic config.h generated by Makefile */' > $@ diff --git a/debian/patches/series b/debian/patches/series index 7df1fc6..b4ead10 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -3,4 +3,3 @@ # destdir.patch tests-pluginpath.patch test-regidx-unsigned-char.patch -fix_config.mk.patch diff --git a/debian/rules b/debian/rules index 00beee4..71cf17c 100755 --- a/debian/rules +++ b/debian/rules @@ -3,10 +3,6 @@ #DH_VERBOSE = 1 #include /usr/share/dpkg/default.mk -export HTSDIR=/usr/include -export USE_GPL=1 -export plugindir=/usr/lib/$(DEB_HOST_MULTIARCH)/bcftools - %: dh $@ --parallel @@ -14,10 +10,23 @@ override_dh_installman: dh_installman --language=C # clean target tries to include config.mk which does not exist inside clean source tree -override_dh_auto_clean: - dh_auto_clean || true - # now it is created but should vanish - rm -f config.mk +clean: config.mk + +config.mk: + $(RM) $@ && touch $@ + +# m4 calls `make print-version` in configure.ac to set the version string. +# If `make` is not silent, this string includes logging messages about changing +# directories due to the way it is invoked, which breaks +# the C compiler test because it introduces a multiline #define statement with +# newlines not escaped. +override_dh_autoreconf: config.mk + export MAKEFLAGS="-s"; dh_autoreconf +#override_dh_auto_configure: override_dh_auto_configure: - dh_auto_configure -- --with-htslib=/usr/lib/htslib + dh_auto_configure -- \ + --with-htslib=system \ + --enable-gsl \ + --with-cblas=gslcblas \ + --with-bcf-plugin-dir=/usr/lib/$(DEB_HOST_MULTIARCH)/bcftools -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit