Andreas Tille pushed to branch master at Debian Med / libseqlib
Commits: d9ecf04c by Andreas Tille at 2018-03-05T16:24:05+01:00 Make sure also private headers of htslib will be installed and usable since these are used in libseqlib-dev - - - - - a46d8dfe by Andreas Tille at 2018-03-05T16:24:32+01:00 Standards-Version: 4.1.3 - - - - - 38ebebcb by Andreas Tille at 2018-03-05T16:24:51+01:00 debhelper 11 - - - - - d15d1594 by Andreas Tille at 2018-03-05T16:45:10+01:00 Upload to unstable - - - - - 5 changed files: - debian/changelog - debian/compat - debian/control - debian/patches/series - + debian/patches/use_private_htslib_headers.patch Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,13 @@ +libseqlib (1.1.1+dfsg-4) unstable; urgency=medium + + * Make sure also private headers of htslib will be installed and usable + since these are used in libseqlib-dev + Closes: #891745 + * Standards-Version: 4.1.3 + * debhelper 11 + + -- Andreas Tille <[email protected]> Mon, 05 Mar 2018 16:25:15 +0100 + libseqlib (1.1.1+dfsg-3) unstable; urgency=medium * Remove liblzma-dev again since it is only used for dist target ===================================== debian/compat ===================================== --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -10 +11 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libhts-private-dev, @@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 10), libbwa-dev (>= 0.7.15-3), libjsoncpp-dev, libssw-dev -Standards-Version: 4.1.2 +Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libseqlib.git Vcs-Git: https://anonscm.debian.org/git/debian-med/libseqlib.git Homepage: https://github.com/walaj/SeqLib @@ -43,6 +43,7 @@ Depends: libseqlib0 (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}, libhts-dev (>= 1.3.2-3), + libhts-private-dev, libjsoncpp-dev, libbwa-dev, libfml-dev ===================================== debian/patches/series ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -7,3 +7,4 @@ dynamic_lib.patch use_debian_packaged_jsoncpp.patch use_debian_packaged_ssw.patch pkg-config.patch +use_private_htslib_headers.patch ===================================== debian/patches/use_private_htslib_headers.patch ===================================== --- /dev/null +++ b/debian/patches/use_private_htslib_headers.patch @@ -0,0 +1,27 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Mon, 05 Mar 2018 15:39:42 +0100 +Bug-Debian: https://bugs.debian.org/891745 +Description: Hack around improper use of private files of htslib + +--- a/SeqLib/BamWalker.h ++++ b/SeqLib/BamWalker.h +@@ -12,8 +12,8 @@ + #endif + + extern "C" { +-#include "htslib/cram/cram.h" +-#include "htslib/cram/cram_io.h" ++#include <htslib/cram/cram.h> ++#include <htslib/cram/cram_io.h> + } + + struct idx_delete { +--- a/libseqlib.pc.in ++++ b/libseqlib.pc.in +@@ -7,5 +7,5 @@ Name: libseqlib + Version: @VERSION@ + Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence data + Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw +-Cflags: -I${includedir} ++Cflags: -I${includedir} -I/usr/include/htslib + View it on GitLab: https://salsa.debian.org/med-team/libseqlib/compare/b03053066a1afb6b25ae0c560584105c8908e3c6...d15d15945f046b947d4218719ae56fede19eaa44 --- View it on GitLab: https://salsa.debian.org/med-team/libseqlib/compare/b03053066a1afb6b25ae0c560584105c8908e3c6...d15d15945f046b947d4218719ae56fede19eaa44 You're receiving this email because of your account on salsa.debian.org.
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