[Debian-med-packaging] Bug#892630: blasr: Please support HDF5 1.10.1

[Gilles Filippini]

Source: blasr
Version: 5.3+0-1
Severity: normal
Tags: patch

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Hi,

Please find attached a patch to support HDF5 1.10.1 currently in experimental.

Thanks in advance,

_g.

- -- System Information:
Distributor ID:	PureOS
Description:	PureOS GNU/Linux 8
Release:	8
Codename:	green
Architecture: x86_64

Kernel: Linux 4.14.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages blasr depends on:
ii  libc6            2.26-6
ii  libgcc1          1:7.2.0-14
ii  libhdf5-100      1.10.0-patch1+docs-4
pn  libhdf5-cpp-100  <none>
pn  libhts2          <none>
pn  libpbbam         <none>
pn  libpbseq         <none>
ii  libstdc++6       7.2.0-14
ii  zlib1g           1:1.2.8.dfsg-5

blasr recommends no packages.

blasr suggests no packages.

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diff -Nru blasr-5.3+0/debian/changelog blasr-5.3+0/debian/changelog
--- blasr-5.3+0/debian/changelog	2016-12-24 02:50:11.000000000 +0100
+++ blasr-5.3+0/debian/changelog	2018-03-09 14:44:37.000000000 +0100
@@ -1,3 +1,10 @@
+blasr (5.3+0-1.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Support for HDF5 1.10.1
+
+ -- Gilles Filippini <pini at debian.org>  Fri, 09 Mar 2018 14:44:37 +0100
+
 blasr (5.3+0-1) unstable; urgency=medium
 
   * Imported Upstream version 5.3+0 (corresponds to smrtanalysis-4.0.0 tag)
diff -Nru blasr-5.3+0/debian/rules blasr-5.3+0/debian/rules
--- blasr-5.3+0/debian/rules	2016-12-20 11:01:23.000000000 +0100
+++ blasr-5.3+0/debian/rules	2018-03-09 14:44:24.000000000 +0100
@@ -20,6 +20,12 @@
 export LIBPBIHDF_INC=$(PBDATA_ROOT_DIR)/hdf
 export LIBPBIHDF_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)
 
+# Needed for HDF5 1.10.1 support
+HDF5_VERSION := $(shell grep 'HDF5 Version' $(HDF5_LIB)/libhdf5.settings | awk '{print $$3}')
+ifeq (yes,$(shell dpkg --compare-versions $(HDF5_VERSION) '>=' 1.10.1 && echo yes))
+export DEB_CXXFLAGS_MAINT_APPEND=-DHAVE_HDF5_1_10_1
+endif
+
 # CPPFLAGS apparently aren't exported for bam2bax/bax2bam
 export DEB_CXXFLAGS_MAINT_PREPEND = $(CPPFLAGS) -I$(PBDATA_ROOT_DIR)