[Debian-med-packaging] Bug#880805: pbseqlib: please support HDF5 1.10.1

[Gilles Filippini]

Source: pbseqlib
Version: 0~20161219-1
Severity: normal
Tags: patch

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Hash: SHA256

Hi,

HDF5 1.10.1 - currently in experimental - introduces non backward compatible
changes in its C++ API, making pbseqlib FTBFS. Please find attached a patch
which support both HDF5 1.10.0 and 1.10.1.

Thanks,

_g.


- -- System Information:
Debian Release: buster/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.13.0-1-amd64 (SMP w/2 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)

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diff -Nru pbseqlib-0~20161219/debian/changelog pbseqlib-0~20161219/debian/changelog
--- pbseqlib-0~20161219/debian/changelog	2016-12-20 09:56:22.000000000 +0100
+++ pbseqlib-0~20161219/debian/changelog	2017-11-04 18:54:19.000000000 +0100
@@ -1,3 +1,11 @@
+pbseqlib (0~20161219-1.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * New patch hdf5-1.10.1-support.patch to cope with HDF5-1.10.1
+    backward incompatible C++ API changes
+
+ -- Gilles Filippini <pini at debian.fr>  Sat, 04 Nov 2017 18:54:19 +0100
+
 pbseqlib (0~20161219-1) unstable; urgency=medium
 
   * Imported Upstream version 0~20161219
diff -Nru pbseqlib-0~20161219/debian/patches/hdf5-1.10.1-support.patch pbseqlib-0~20161219/debian/patches/hdf5-1.10.1-support.patch
--- pbseqlib-0~20161219/debian/patches/hdf5-1.10.1-support.patch	1970-01-01 01:00:00.000000000 +0100
+++ pbseqlib-0~20161219/debian/patches/hdf5-1.10.1-support.patch	2017-11-04 18:17:47.000000000 +0100
@@ -0,0 +1,72 @@
+Description: cope with HDF5 C++ API changes in release 1.10.1
+ From HDF5 upstream commits c78f1ec8829 and b1c4fd77d9c:
+ .
+ [svn-r30309] Purpose: Fix bug HDFFR-9920
+ Description:
+    Rearranged the classes to model the relationship of HDF5 objects more
+    accurately.  The changes included:
+    - moved CommonFG's methods to Group
+    - removed CommonFG from Group's base class list
+    - removed CommonFG from H5File's base class list and changed
+      "public H5Location" to "public Group" in the base class list
+    - CommonFG became unused
+    - result of the modified partial class diagram:
+ .
+                                IdComponent
+                                     |
+                                H5Location
+                                /
+                        H5Object
+                           |
+                        /  /  \
+                DadaType Group DataSet
+                          |
+                        H5File
+ .
+ [svn-r30311] Purpose: Fix bug HDFFR-9920 cont.
+ Description:
+    Continued rearranging the classes to model the relationship of HDF5
+    objects more accurately.  The changes included:
+    - in the baseclass list of Attribute, changed "public IdComponent" to
+      "public H5Location", because location sometime can be specified with
+      attribute
+    - moved H5A wrappers in H5Location to H5Object because H5A functions
+      can't be called on attribute id
+    - removed the stubs Attribute::iterateAttrs and Attribute::renameAttr
+    - removed Attribute::getFileName and Attribute::flush, because
+          H5Location has them
+    - result of the modified partial class diagram, regarding Attribute
+ .
+                                IdComponent
+                                     |
+                                H5Location   AbstractDs
+                                /       \   /
+                        H5Object     Attribute
+Author: Gilles Filippini <pini at debian.org>
+Index: pbseqlib/hdf/HDFConfig.hpp
+===================================================================
+--- pbseqlib.orig/hdf/HDFConfig.hpp
++++ pbseqlib/hdf/HDFConfig.hpp
+@@ -3,5 +3,10 @@
+ 
+ #define MAX_DIMS 10
+ 
++#ifdef HAVE_HDF5_1_10_1
++#define CommonFG Group
++#define H5Location H5Object
++#endif
++
+ 
+ #endif
+Index: pbseqlib/hdf/HDFAttributable.hpp
+===================================================================
+--- pbseqlib.orig/hdf/HDFAttributable.hpp
++++ pbseqlib/hdf/HDFAttributable.hpp
+@@ -5,6 +5,7 @@
+ #include <vector>
+ #include <H5Cpp.h>
+ #include <H5Location.h>
++#include "HDFConfig.hpp"
+ 
+ void CallStoreAttributeName(H5::H5Location &obj, std::string attrName, void *attrListPtr);
+ 
diff -Nru pbseqlib-0~20161219/debian/patches/series pbseqlib-0~20161219/debian/patches/series
--- pbseqlib-0~20161219/debian/patches/series	1970-01-01 01:00:00.000000000 +0100
+++ pbseqlib-0~20161219/debian/patches/series	2017-10-12 21:39:30.000000000 +0200
@@ -0,0 +1 @@
+hdf5-1.10.1-support.patch
diff -Nru pbseqlib-0~20161219/debian/rules pbseqlib-0~20161219/debian/rules
--- pbseqlib-0~20161219/debian/rules	2016-12-20 08:48:57.000000000 +0100
+++ pbseqlib-0~20161219/debian/rules	2017-11-04 18:35:46.000000000 +0100
@@ -13,6 +13,12 @@
 
 export LDLIBS += -lpbbam
 
+# Needed for patch hdf5-1.10.1-support.patch
+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_CPPFLAGS_MAINT_APPEND=-DHAVE_HDF5_1_10_1
+endif
+
 %:
 	dh $@