Your message dated Fri, 10 Nov 2017 04:05:42 +0000
with message-id <[email protected]>
and subject line Bug#880805: fixed in pbseqlib 0~20161219-2
has caused the Debian Bug report #880805,
regarding pbseqlib: please support HDF5 1.10.1
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
880805: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=880805
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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)
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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 <[email protected]> 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 <[email protected]>
+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 $@
--- End Message ---
--- Begin Message ---
Source: pbseqlib
Source-Version: 0~20161219-2
We believe that the bug you reported is fixed in the latest version of
pbseqlib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Afif Elghraoui <[email protected]> (supplier of updated pbseqlib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 09 Nov 2017 22:48:55 -0500
Source: pbseqlib
Binary: libpbseq libpbseq-dev libpbdata-dev libpbdata libpbihdf-dev libpbihdf
libblasr-dev libblasr
Architecture: source
Version: 0~20161219-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Afif Elghraoui <[email protected]>
Description:
libblasr - tools for aligning PacBio reads to target sequences
libblasr-dev - tools for aligning PacBio reads to target sequences (development
libpbdata - tools for handling PacBio sequences
libpbdata-dev - tools for handling PacBio sequences (development files)
libpbihdf - tools for handling PacBio hdf5 files
libpbihdf-dev - tools for handling PacBio hdf5 files (development files)
libpbseq - library for analyzing PacBio sequencing data
libpbseq-dev - library for analyzing PacBio sequencing data (development files)
Closes: 880805
Changes:
pbseqlib (0~20161219-2) unstable; urgency=medium
.
* Add support for HDF5 1.10.1
Thanks to Gilles Filippini for the patches (Closes: #880805)
* Bump Standards-Version to 4.1.1
* Update copyright year
* Handle nocheck build profile
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