Source: pbseqlib Version: 0~20161219-1 Severity: normal Tags: patch -----BEGIN PGP SIGNED MESSAGE----- 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) -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAln+K6YACgkQ7+hsbH/+ z4Mc+gf+OIHBUnTS9HegsJVNIk5A7OO59Y5IzRnJd0/9scEo2wBCk7/lSiCD/Pw5 NS928v8IXXSEqOsNG+nMYmjHts7BD5oBR9vPudJvmXgPpKrM9CssYi6B5Pou89+i 4xS4bxxFAavjVEF+O+mtFBCi6xl3bUI/7vaTK/221nKC5lr0LTPM1KPFkSOWYI71 QGRYRrDT2OsoitiUdiBmCLE4tV0Hrd8p/pVy0cnHE1U3d2aSKsUPPGwWsOPh7cCj GzcLuZy4/vuz+FuJBBgPBUt5tPXSBwD+8/faYLdxDQDBBWrR642n4ndxZxOmpRpT jru6BHtoY0LOuLO/5sI62bDFFVsAZg== =co+D -----END PGP SIGNATURE-----
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 <p...@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 <p...@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 $@