[Git][debian-gis-team/hdf5][master] Ack change by Bas

[Gilles Filippini]

Gilles Filippini pushed to branch master at Debian GIS Project / hdf5


Commits:
67de0bb1 by Gilles Filippini at 2018-04-06T23:18:19+02:00
Ack change by Bas

- - - - -


1 changed file:

- debian/changelog


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,6 @@
 hdf5 (1.10.2+repack-1~exp2) UNRELEASED; urgency=medium
 
+  [ Bas Couwenberg ]
   * Remove trailing comma from dependency list.
 
  -- Gilles Filippini <p...@debian.org>  Tue, 03 Apr 2018 22:05:51 +0200



View it on GitLab: 
https://salsa.debian.org/debian-gis-team/hdf5/commit/67de0bb19434e79486eaf19072cd5926cac80bdd

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[Git][debian-gis-team/hdf5] Pushed new tag debian/1.10.2+repack-1_exp1

[Gilles Filippini]

Gilles Filippini pushed new tag debian/1.10.2+repack-1_exp1 at Debian GIS 
Project / hdf5

---
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[Git][debian-gis-team/hdf5] Pushed new tag upstream/1.10.2+repack

[Gilles Filippini]

Gilles Filippini pushed new tag upstream/1.10.2+repack at Debian GIS Project / 
hdf5

---
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[Git][debian-gis-team/hdf5][upstream] New upstream version 1.10.2+repack

[Gilles Filippini]

Gilles Filippini pushed to branch upstream at Debian GIS Project / hdf5


Commits:
555edfac by Gilles Filippini at 2018-04-02T13:28:09+02:00
New upstream version 1.10.2+repack
- - - - -


30 changed files:

- CMakeFilters.cmake
- CMakeInstallation.cmake
- CMakeLists.txt
- COPYING
- CTestConfig.cmake
- MANIFEST
- Makefile.in
- README.txt
- autogen.sh
- bin/h5vers
- bin/release
- bin/trace
- c++/CMakeLists.txt
- c++/Makefile.in
- c++/examples/CMakeLists.txt
- c++/examples/CMakeTests.cmake
- c++/examples/Makefile.in
- c++/examples/chunks.cpp
- c++/examples/compound.cpp
- c++/examples/create.cpp
- c++/examples/extend_ds.cpp
- c++/examples/h5group.cpp
- c++/examples/h5tutr_cmprss.cpp
- c++/examples/h5tutr_crtatt.cpp
- c++/examples/h5tutr_crtdat.cpp
- c++/examples/h5tutr_crtgrp.cpp
- c++/examples/h5tutr_crtgrpar.cpp
- c++/examples/h5tutr_crtgrpd.cpp
- c++/examples/h5tutr_extend.cpp
- c++/examples/h5tutr_rdwt.cpp


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/debian-gis-team/hdf5/commit/555edfac3fd45aa6fe28148ea90335fdfbe5b0fb

---
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[Git][debian-gis-team/hdf5][pristine-tar] pristine-tar data for hdf5_1.10.2+repack.orig.tar.gz

[Gilles Filippini]

Gilles Filippini pushed to branch pristine-tar at Debian GIS Project / hdf5


Commits:
904b57f0 by Gilles Filippini at 2018-04-02T13:29:31+02:00
pristine-tar data for hdf5_1.10.2+repack.orig.tar.gz

- - - - -


2 changed files:

- + hdf5_1.10.2+repack.orig.tar.gz.delta
- + hdf5_1.10.2+repack.orig.tar.gz.id


Changes:

=
hdf5_1.10.2+repack.orig.tar.gz.delta
=
Binary files /dev/null and b/hdf5_1.10.2+repack.orig.tar.gz.delta differ


=
hdf5_1.10.2+repack.orig.tar.gz.id
=
--- /dev/null
+++ b/hdf5_1.10.2+repack.orig.tar.gz.id
@@ -0,0 +1 @@
+faeda1ac0e4f7a9ae137f96be0dd2c0b044c2f50



View it on GitLab: 
https://salsa.debian.org/debian-gis-team/hdf5/commit/904b57f0d5f2149e8cf1280e492c922df2e8d57e

---
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[Git][debian-gis-team/hdf5][master] 13 commits: Prepare import-orig of release 1.10.2

[Gilles Filippini]

Gilles Filippini pushed to branch master at Debian GIS Project / hdf5


Commits:
76093348 by Gilles Filippini at 2018-04-02T13:27:40+02:00
Prepare import-orig of release 1.10.2

- - - - -
555edfac by Gilles Filippini at 2018-04-02T13:28:09+02:00
New upstream version 1.10.2+repack
- - - - -
42f8f04a by Gilles Filippini at 2018-04-02T13:29:33+02:00
Merge tag upstream/1.10.2+repack

Upstream version 1.10.2+repack

- - - - -
efbab557 by Gilles Filippini at 2018-04-02T13:58:30+02:00
Refresh patches

- - - - -
38cc1be3 by Gilles Filippini at 2018-04-02T14:41:28+02:00
Update debian.control

- - - - -
b7461535 by Gilles Filippini at 2018-04-02T16:51:48+02:00
Force update of debian/control

- - - - -
e256edd0 by Gilles Filippini at 2018-04-02T17:02:55+02:00
Bump SONAME_CXX

- - - - -
fbbbd83e by Gilles Filippini at 2018-04-02T18:20:38+02:00
Update symbols files

- - - - -
e497f199 by Gilles Filippini at 2018-04-02T21:42:24+02:00
Fix shlibs

- - - - -
5269097b by Gilles Filippini at 2018-04-02T23:44:28+02:00
Java lib: target Java 1.8

- - - - -
ec055566 by Gilles Filippini at 2018-04-03T20:09:34+02:00
Update lintian-overrides

- - - - -
031dea32 by Gilles Filippini at 2018-04-03T20:13:53+02:00
Remove missing symbols from symbols files

- - - - -
2ddeb428 by Gilles Filippini at 2018-04-03T20:51:36+02:00
Upload release 1.10.2+repack-1~exp1 to experimental

- - - - -


30 changed files:

- CMakeFilters.cmake
- CMakeInstallation.cmake
- CMakeLists.txt
- COPYING
- CTestConfig.cmake
- MANIFEST
- Makefile.in
- README.txt
- autogen.sh
- bin/h5vers
- bin/release
- bin/trace
- c++/CMakeLists.txt
- c++/Makefile.in
- c++/examples/CMakeLists.txt
- c++/examples/CMakeTests.cmake
- c++/examples/Makefile.in
- c++/examples/chunks.cpp
- c++/examples/compound.cpp
- c++/examples/create.cpp
- c++/examples/extend_ds.cpp
- c++/examples/h5group.cpp
- c++/examples/h5tutr_cmprss.cpp
- c++/examples/h5tutr_crtatt.cpp
- c++/examples/h5tutr_crtdat.cpp
- c++/examples/h5tutr_crtgrp.cpp
- c++/examples/h5tutr_crtgrpar.cpp
- c++/examples/h5tutr_crtgrpd.cpp
- c++/examples/h5tutr_extend.cpp
- c++/examples/h5tutr_rdwt.cpp


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/debian-gis-team/hdf5/compare/005eedce9f922c6fe69474ac6dfa03e9d3c2625f...2ddeb4281173fb5529b8cfda99a05148213389b1

---
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[Git][debian-gis-team/hdf5] Pushed new branch stretch

[Gilles Filippini]

Gilles Filippini pushed new branch stretch at Debian GIS Project / hdf5

---
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Bug#871506: stretch update for hdf5

[Gilles Filippini]

Sebastiaan Couwenberg a écrit le 26/02/2018 à 22:33 :
> On 02/26/2018 10:23 PM, Adrian Bunk wrote:
>> On Sun, Aug 13, 2017 at 05:51:08PM +, Debian Bug Tracking System wrote:
>>> ...
>>>  hdf5 (1.10.0-patch1+docs-4) unstable; urgency=medium
>>>  .
>>>* debian/rules: fix javahelper invocation (closes: #871506)
>>> ...
>>
>> Thanks a lot for fixing this bug for unstable.
>>
>> It is still present in stretch, could you also fix it there?
>> Alternatively, I can fix it for stretch if you don't object.
> 
> The stretch-pu was requested in #872642 and given a go-ahead.
> 
> It's just a matter of uploading or am I missing something?

Oops! I missed the go which occurred while I was on holidays this last
summer. Sorry about that.

I'll take care of it in the next few days.

Thanks,

_g.



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[Git][debian-gis-team/hdf5] Deleted branch jessie

[Gilles Filippini]

Gilles Filippini deleted branch jessie at Debian GIS Project / hdf5

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[Git][debian-gis-team/hdf5] Pushed new branch jessie

[Gilles Filippini]

Gilles Filippini pushed new branch jessie at Debian GIS Project / hdf5

---
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[Git][debian-gis-team/hdf5][pristine-tar] 2 commits: pristine-tar data for hdf5_1.10.1+docs.orig.tar.gz

[Gilles Filippini]

Gilles Filippini pushed to branch pristine-tar at Debian GIS Project / hdf5


Commits:
6936e346 by Gilles Filippini at 2017-10-03T23:51:38+02:00
pristine-tar data for hdf5_1.10.1+docs.orig.tar.gz

- - - - -
465fb5cf by Gilles Filippini at 2018-01-14T15:49:58+01:00
pristine-tar data for hdf5_1.10.1+repack.orig.tar.gz

- - - - -


4 changed files:

- + hdf5_1.10.1+docs.orig.tar.gz.delta
- + hdf5_1.10.1+docs.orig.tar.gz.id
- + hdf5_1.10.1+repack.orig.tar.gz.delta
- + hdf5_1.10.1+repack.orig.tar.gz.id


Changes:

=
hdf5_1.10.1+docs.orig.tar.gz.delta
=
Binary files /dev/null and b/hdf5_1.10.1+docs.orig.tar.gz.delta differ


=
hdf5_1.10.1+docs.orig.tar.gz.id
=
--- /dev/null
+++ b/hdf5_1.10.1+docs.orig.tar.gz.id
@@ -0,0 +1 @@
+6e1213928bd8607c736ccdbd614c17628567adeb


=
hdf5_1.10.1+repack.orig.tar.gz.delta
=
Binary files /dev/null and b/hdf5_1.10.1+repack.orig.tar.gz.delta differ


=
hdf5_1.10.1+repack.orig.tar.gz.id
=
--- /dev/null
+++ b/hdf5_1.10.1+repack.orig.tar.gz.id
@@ -0,0 +1 @@
+4ee9fd63385fdbafd1a3db8bd5537e0b7554aaa9



View it on GitLab: 
https://salsa.debian.org/debian-gis-team/hdf5/compare/b0b03b775326fbdfd805ab3f874160664a349019...465fb5cfecc2c963488592978ec2536d71cc54b9

---
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[Git][debian-gis-team/hdf5][master] debian/control: make Vcs-* fields point to salsa.debian.org

[Gilles Filippini]

Gilles Filippini pushed to branch master at Debian GIS Project / hdf5


Commits:
13001935 by Gilles Filippini at 2018-02-18T16:53:23+01:00
debian/control: make Vcs-* fields point to salsa.debian.org

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,13 @@
 hdf5 (1.10.1+repack-1~exp2) UNRELEASED; urgency=medium
 
+  [ Bas Couwenberg ]
   * Team upload.
   * Add gbp.conf to use pristine-tar by default.
   * Fix deprecated source override location.
 
+  [ Gilles Filippini ]
+  * debian/control: make Vcs-* fields point to salsa.debian.org
+
  -- Bas Couwenberg <sebas...@debian.org>  Sat, 10 Feb 2018 11:35:42 +0100
 
 hdf5 (1.10.1+repack-1~exp1) experimental; urgency=medium


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -13,8 +13,8 @@ Build-Depends-Indep:
  doxygen, php-cli,
 Standards-Version: 3.9.8
 Homepage: http://hdfgroup.org/HDF5/
-Vcs-Browser: https://anonscm.debian.org/cgit/pkg-grass/hdf5.git
-Vcs-Git: https://anonscm.debian.org/git/pkg-grass/hdf5.git
+Vcs-Git: https://salsa.debian.org/debian-gis-team/hdf5.git
+Vcs-Browser: https://salsa.debian.org/debian-gis-team/hdf5
 
 Package: libhdf5-101
 Section: libs



View it on GitLab: 
https://salsa.debian.org/debian-gis-team/hdf5/commit/130019359d8cafcb481573e0df5fab2a1ea59c47

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[hdf5] 03/05: Merge tag 'upstream/1.10.1+repack'

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 25bd1e196951841a954b83f9b9603ba578840257
Merge: 5548940 f8a4421
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Jan 14 15:49:58 2018 +0100

Merge tag 'upstream/1.10.1+repack'

Upstream version 1.10.1+repack

 .autom4te.cfg   |  18 +
 .h5chkright.ini |  54 ++
 Makefile|  35 --
 bin/README  |   2 +
 bin/bbrelease   | 411 ++
 bin/checkapi|  65 +++
 bin/checkposix  | 113 
 bin/chkconfigure|  82 +++
 bin/chkcopyright| 866 
 bin/debug-ohdr  |  38 ++
 bin/errors  | 138 +
 bin/gcov_script |  51 ++
 bin/pkgscrpts/h5rmflags | 165 ++
 bin/pkgscrpts/makeHDF5BinaryTarfiles.pl | 366 
 bin/pkgscrpts/makeInternalREADME.pl | 215 +++
 bin/pkgscrpts/makeOuterREADME.pl| 182 ++
 bin/runtest | 966 
 bin/snapshot_version|  19 +
 bin/switch_maint_mode   |  81 +++
 bin/timekeeper  | 129 +
 src/.indent.pro | 150 +
 src/hdf5-lin.lnt|  24 +
 src/hdf5-win.lnt|  39 ++
 src/hdf5.lnt|  90 +++
 24 files changed, 4264 insertions(+), 35 deletions(-)

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[hdf5] 04/05: debian/rules: fix version mangling regarding +repack

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit edf3baf1bc93161eabcdcbf13ca4d758cebd973e
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Jan 14 16:53:45 2018 +0100

debian/rules: fix version mangling regarding +repack
---
 debian/rules | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/rules b/debian/rules
index 61d79c7..d7f068e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,8 +17,8 @@
 
 package = libhdf5
 pkgversion ?= $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-upstreamversion ?= $(shell echo $(pkgversion) | sed -r 
's/^([0-9\.]*)([-~][^-~+]*)?(\+docs[0-9]*)?-[^-]*$$/\1\2/')
-libversion ?= $(shell echo $(pkgversion) | sed -r 
's/^([0-9\.]*)([-~][^-~+]*)?(\+docs[0-9]*)?-[^-]*$$/\1/')
+upstreamversion ?= $(shell echo $(pkgversion) | sed -r 
's/^([0-9\.]*)([-~][^-~+]*)?(\+repack[0-9]*)?-[^-]*$$/\1\2/')
+libversion ?= $(shell echo $(pkgversion) | sed -r 
's/^([0-9\.]*)([-~][^-~+]*)?(\+repack[0-9]*)?-[^-]*$$/\1/')
 
 # BEGIN - Get sonames from config/lt_vers.am
 include config/lt_vers.am

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[hdf5] 01/05: Fix debian/watch and prepare import of upstream release 1.10.1+repack

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 55489403f41c162a666ccb103b83229e275d8b3f
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Jan 14 14:39:32 2018 +0100

Fix debian/watch and prepare import of upstream release 1.10.1+repack
---
 debian/changelog|  4 +++-
 debian/orig-tar.exclude |  1 +
 debian/orig-tar.sh  | 11 ++-
 debian/watch|  9 -
 4 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index df9351c..cf45a14 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,7 @@
-hdf5 (1.10.1+docs-1~exp3) UNRELEASED; urgency=medium
+hdf5 (1.10.1+repack-1~exp1) UNRELEASED; urgency=medium
 
+  * Fix broken debian/watch due to upstrem web site major change; the
+uscan download mode is now set to git
   * Disable dh_auto_test on ppc64el (HDFFV-10309)
   * This upstream release fixes openmpi flavor on arm64 (closes: #855810)
   * Priority: replace 'extra' with 'optional'
diff --git a/debian/orig-tar.exclude b/debian/orig-tar.exclude
index 0ba464d..6163353 100644
--- a/debian/orig-tar.exclude
+++ b/debian/orig-tar.exclude
@@ -1,3 +1,4 @@
+.git*
 html/PSandPDF
 html/Specifications
 html/HL/Examples
diff --git a/debian/orig-tar.sh b/debian/orig-tar.sh
index 717b526..2fd908e 100755
--- a/debian/orig-tar.sh
+++ b/debian/orig-tar.sh
@@ -1,17 +1,18 @@
 #!/bin/sh
 # Called from uscan with parameters:
-# --upstream-version  
+# --upstream-version 
 #
 # Require git
 set -e
 
 UPSTREAM_VERSION="$2"
-MANGLED_UPSTREAM_VERSION="$(echo "$UPSTREAM_VERSION" | sed 
's/-\(alpha\|pre\)/~\1/')+docs"
+MANGLED_UPSTREAM_VERSION="$(echo "$UPSTREAM_VERSION" | sed 
's/-\(alpha\|pre\)/~\1/')+repack"
 UPSTREAM_DOC_VERSION="${UPSTREAM_VERSION%-*}"
 if [ "$UPSTREAM_DOC_VERSION" = 1.10.0 ]; then
   UPSTREAM_DOC_VERSION=1.10
 fi
-PACKAGE=$(basename "$3" "_$UPSTREAM_VERSION.orig.tar.gz")
+PACKAGE=hdf5
+DOWNLOADED_TARBALL=../${PACKAGE}_${UPSTREAM_VERSION}.orig.tar.gz
 
 SOURCE_DIR="$PACKAGE-$UPSTREAM_VERSION"
 DEBIAN_SOURCE_DIR="$PACKAGE-$MANGLED_UPSTREAM_VERSION"
@@ -19,7 +20,7 @@ TAR="../${PACKAGE}_$MANGLED_UPSTREAM_VERSION.orig.tar.gz"
 HTML_DIR="$DEBIAN_SOURCE_DIR/html"
 
 # extract the upstream archive
-tar xf $3
+tar xf $DOWNLOADED_TARBALL
 
 # get docs
 git clone --depth 1 --single-branch --branch hdf5_"$(echo 
"$UPSTREAM_DOC_VERSION" | sed 's/\./_/g')" 
https://bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
@@ -35,6 +36,6 @@ find "$HTML_DIR" -type d -empty -delete
 
 # repack into orig.tar.gz
 tar -c -z -f "$TAR" "$DEBIAN_SOURCE_DIR/"
-rm -rf "$SOURCE_DIR" "$DEBIAN_SOURCE_DIR" "$3"
+rm -rf "$SOURCE_DIR" "$DEBIAN_SOURCE_DIR" "$(readlink -f 
"$DOWNLOADED_TARBALL")" "$DOWNLOADED_TARBALL" ../${PACKAGE}.[1-9]*.git
 
 echo "$PACKAGE: downloaded docs and renamed archive to $(basename "$TAR")"
diff --git a/debian/watch b/debian/watch
index 930e239..a32764a 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,5 +1,4 @@
-version=3
-opts="dversionmangle=s/\+docs\d*$//;s/~(alpha|pre)/-\\1/,dirversionmangle=s/-(alpha|pre)/~\\1/"
 \
-   ftp://ftp.hdfgroup.org/HDF5/releases/hdf5-(.*)/hdf5-(.*)/src/ \
-   hdf5-(.*).tar.gz \
-   debian debian/orig-tar.sh
+version=4
+opts="mode=git, pgpmode=none, compression=gz, 
dversionmangle=s/\+(docs|repack)\d*$//;s/~(alpha|pre)/-\\1/, 
uversionmangle=s/_/./g" \
+   https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git \
+   refs/tags/hdf5-([\d_]+) debian debian/orig-tar.sh

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[hdf5] annotated tag debian/1.10.1+repack-1_exp1 created (now 981a026)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.1+repack-1_exp1
in repository hdf5.

at  981a026   (tag)
   tagging  f22652bc05a7a32a94c04bdab3355324cff193ff (commit)
  replaces  debian/1.10.1+docs-1_exp2
 tagged by  Gilles Filippini
on  Sun Jan 14 17:18:14 2018 +0100

- Log -
hdf5 Debian release 1.10.1+repack-1~exp1

Gilles Filippini (8):
  Disable dh_auto_test on ppc64el (HDFFV-10309)
  closes: #855810
  Priority: replace 'extra' with 'optional'
  Fix debian/watch and prepare import of upstream release 1.10.1+repack
  New upstream version 1.10.1+repack
  Merge tag 'upstream/1.10.1+repack'
  debian/rules: fix version mangling regarding +repack
  Upload release 1.10.1+repack-1~exp1 to experimental

---

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[hdf5] branch upstream updated (173f2a1 -> f8a4421)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch upstream
in repository hdf5.

  from  173f2a1   New upstream version 1.10.1+docs
   new  f8a4421   New upstream version 1.10.1+repack

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 config/linux-gnuaout => .autom4te.cfg |  11 +-
 .h5chkright.ini   |  54 ++
 Makefile  |  35 --
 bin/README|   2 +
 bin/bbrelease | 411 +
 bin/checkapi  |  65 ++
 bin/checkposix| 113 
 bin/chkconfigure  |  82 +++
 bin/chkcopyright  | 866 ++
 tools/src/Makefile.am => bin/debug-ohdr   |  34 +-
 bin/errors| 138 +
 bin/gcov_script   |  51 ++
 bin/pkgscrpts/h5rmflags   | 165 +
 bin/pkgscrpts/makeHDF5BinaryTarfiles.pl   | 366 +++
 bin/pkgscrpts/makeInternalREADME.pl   | 215 +++
 bin/pkgscrpts/makeOuterREADME.pl  | 182 ++
 bin/runtest   | 966 ++
 tools/Makefile.am => bin/snapshot_version |  20 +-
 bin/switch_maint_mode |  81 +++
 bin/timekeeper| 129 
 src/.indent.pro   | 150 +
 src/hdf5-lin.lnt  |  24 +
 src/hdf5-win.lnt  |  39 ++
 src/hdf5.lnt  |  90 +++
 24 files changed, 4223 insertions(+), 66 deletions(-)
 copy config/linux-gnuaout => .autom4te.cfg (77%)
 create mode 100644 .h5chkright.ini
 delete mode 100644 Makefile
 create mode 100644 bin/README
 create mode 100755 bin/bbrelease
 create mode 100755 bin/checkapi
 create mode 100755 bin/checkposix
 create mode 100755 bin/chkconfigure
 create mode 100755 bin/chkcopyright
 copy tools/src/Makefile.am => bin/debug-ohdr (50%)
 mode change 100644 => 100755
 create mode 100755 bin/errors
 create mode 100755 bin/gcov_script
 create mode 100755 bin/pkgscrpts/h5rmflags
 create mode 100755 bin/pkgscrpts/makeHDF5BinaryTarfiles.pl
 create mode 100755 bin/pkgscrpts/makeInternalREADME.pl
 create mode 100755 bin/pkgscrpts/makeOuterREADME.pl
 create mode 100755 bin/runtest
 copy tools/Makefile.am => bin/snapshot_version (67%)
 create mode 100755 bin/switch_maint_mode
 create mode 100755 bin/timekeeper
 create mode 100644 src/.indent.pro
 create mode 100644 src/hdf5-lin.lnt
 create mode 100644 src/hdf5-win.lnt
 create mode 100644 src/hdf5.lnt

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[hdf5] 05/05: Upload release 1.10.1+repack-1~exp1 to experimental

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit f22652bc05a7a32a94c04bdab3355324cff193ff
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Jan 14 16:54:42 2018 +0100

Upload release 1.10.1+repack-1~exp1 to experimental
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index cf45a14..bbdd57d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-hdf5 (1.10.1+repack-1~exp1) UNRELEASED; urgency=medium
+hdf5 (1.10.1+repack-1~exp1) experimental; urgency=medium
 
   * Fix broken debian/watch due to upstrem web site major change; the
 uscan download mode is now set to git
@@ -6,7 +6,7 @@ hdf5 (1.10.1+repack-1~exp1) UNRELEASED; urgency=medium
   * This upstream release fixes openmpi flavor on arm64 (closes: #855810)
   * Priority: replace 'extra' with 'optional'
 
- -- Gilles Filippini <p...@debian.org>  Mon, 23 Oct 2017 20:01:47 +0200
+ -- Gilles Filippini <p...@debian.org>  Sun, 14 Jan 2018 16:54:08 +0100
 
 hdf5 (1.10.1+docs-1~exp2) experimental; urgency=medium
 

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[hdf5] annotated tag upstream/1.10.1+repack created (now a427c10)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag upstream/1.10.1+repack
in repository hdf5.

at  a427c10   (tag)
   tagging  f8a4421e43f8fa7cc9db9aba73e9bd35a5bed3e7 (commit)
  replaces  upstream/1.10.1+docs
 tagged by  Gilles Filippini
on  Sun Jan 14 15:49:58 2018 +0100

- Log -
Upstream version 1.10.1+repack

Gilles Filippini (1):
  New upstream version 1.10.1+repack

---

No new revisions were added by this update.

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[hdf5] 01/01: pristine-tar data for hdf5_1.10.1+repack.orig.tar.gz

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch pristine-tar
in repository hdf5.

commit 465fb5cfecc2c963488592978ec2536d71cc54b9
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Jan 14 15:49:58 2018 +0100

pristine-tar data for hdf5_1.10.1+repack.orig.tar.gz
---
 hdf5_1.10.1+repack.orig.tar.gz.delta | Bin 0 -> 139683 bytes
 hdf5_1.10.1+repack.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/hdf5_1.10.1+repack.orig.tar.gz.delta 
b/hdf5_1.10.1+repack.orig.tar.gz.delta
new file mode 100644
index 000..6d7f5cd
Binary files /dev/null and b/hdf5_1.10.1+repack.orig.tar.gz.delta differ
diff --git a/hdf5_1.10.1+repack.orig.tar.gz.id 
b/hdf5_1.10.1+repack.orig.tar.gz.id
new file mode 100644
index 000..4e3a31c
--- /dev/null
+++ b/hdf5_1.10.1+repack.orig.tar.gz.id
@@ -0,0 +1 @@
+4ee9fd63385fdbafd1a3db8bd5537e0b7554aaa9

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[hdf5] 02/05: New upstream version 1.10.1+repack

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit f8a4421e43f8fa7cc9db9aba73e9bd35a5bed3e7
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Jan 14 15:48:36 2018 +0100

New upstream version 1.10.1+repack
---
 .autom4te.cfg   |  18 +
 .h5chkright.ini |  54 ++
 Makefile|  35 --
 bin/README  |   2 +
 bin/bbrelease   | 411 ++
 bin/checkapi|  65 +++
 bin/checkposix  | 113 
 bin/chkconfigure|  82 +++
 bin/chkcopyright| 866 
 bin/debug-ohdr  |  38 ++
 bin/errors  | 138 +
 bin/gcov_script |  51 ++
 bin/pkgscrpts/h5rmflags | 165 ++
 bin/pkgscrpts/makeHDF5BinaryTarfiles.pl | 366 
 bin/pkgscrpts/makeInternalREADME.pl | 215 +++
 bin/pkgscrpts/makeOuterREADME.pl| 182 ++
 bin/runtest | 966 
 bin/snapshot_version|  19 +
 bin/switch_maint_mode   |  81 +++
 bin/timekeeper  | 129 +
 src/.indent.pro | 150 +
 src/hdf5-lin.lnt|  24 +
 src/hdf5-win.lnt|  39 ++
 src/hdf5.lnt|  90 +++
 24 files changed, 4264 insertions(+), 35 deletions(-)

diff --git a/.autom4te.cfg b/.autom4te.cfg
new file mode 100644
index 000..e7c2ec1
--- /dev/null
+++ b/.autom4te.cfg
@@ -0,0 +1,18 @@
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# h...@hdfgroup.org.
+
+## -- ##
+## User Preferences.  ##
+## -- ##
+
+begin-language: "Autoconf"
+args: --no-cache
+end-language: "Autoconf"
diff --git a/.h5chkright.ini b/.h5chkright.ini
new file mode 100644
index 000..1010dce
--- /dev/null
+++ b/.h5chkright.ini
@@ -0,0 +1,54 @@
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# h...@hdfgroup.org.
+
+# Initialization files for the Copyright Checker, chkcopyright.
+# Each line is a keyword for action and the rest are values.
+# Keywords:
+# '#'  Comments
+# skip Files to be skipped
+# pruneDirectories to be skipped.  Notice this prunes all 
directories
+#  with the same name.  E.g.,
+#  "prune test" skips test, fortran/test, c++/test, ...
+
+# Skip COPYING since it is the detail Copyright notice.
+skip COPYING
+
+# Sort of strange to have a copyright notice in README
+skip README
+
+# Non-UI copyrighted files in top-level
+skip aclocal.m4
+
+# Non-UI copyrighted files in bin.
+skip config.guess
+skip config.sub
+skip depcomp
+skip install-sh
+skip ltmain.sh
+skip missing
+skip mkinstalldirs
+
+# Generated files in top-level
+skip configure
+
+# Generated files in src.
+skip H5config.h.in
+
+# Generated files in fortran/src.
+skip H5match_types.c
+skip H5test_kind.f90
+
+# Ignore this expected output file in windows/examples.
+skip testExamples_exp_output.txt
+
+# Skip all testfiles/* since if we insert a copyright notice in the expected
+# data files, we would have to spend extra effort to filter them out.
+prune testfiles
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 9edb476..000
--- a/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-# Top-level distributed Makefile  -*- makefile -*-
-
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the COPYING file, which can be found at the root of the source code
-# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
-#

[hdf5] branch pristine-tar updated (6936e34 -> 465fb5c)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch pristine-tar
in repository hdf5.

  from  6936e34   pristine-tar data for hdf5_1.10.1+docs.orig.tar.gz
   new  465fb5c   pristine-tar data for hdf5_1.10.1+repack.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 hdf5_1.10.1+repack.orig.tar.gz.delta | Bin 0 -> 139683 bytes
 hdf5_1.10.1+repack.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 hdf5_1.10.1+repack.orig.tar.gz.delta
 create mode 100644 hdf5_1.10.1+repack.orig.tar.gz.id

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[hdf5] branch master updated (d5f9a09 -> f22652b)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master
in repository hdf5.

  from  d5f9a09   Priority: replace 'extra' with 'optional'
   new  5548940   Fix debian/watch and prepare import of upstream release 
1.10.1+repack
   new  f8a4421   New upstream version 1.10.1+repack
   new  25bd1e1   Merge tag 'upstream/1.10.1+repack'
   new  edf3baf   debian/rules: fix version mangling regarding +repack
   new  f22652b   Upload release 1.10.1+repack-1~exp1 to experimental

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 config/linux-gnuaout => .autom4te.cfg |  11 +-
 .h5chkright.ini   |  54 ++
 Makefile  |  35 --
 bin/README|   2 +
 bin/bbrelease | 411 +
 bin/checkapi  |  65 ++
 bin/checkposix| 113 
 bin/chkconfigure  |  82 +++
 bin/chkcopyright  | 866 ++
 tools/src/Makefile.am => bin/debug-ohdr   |  34 +-
 bin/errors| 138 +
 bin/gcov_script   |  51 ++
 bin/pkgscrpts/h5rmflags   | 165 +
 bin/pkgscrpts/makeHDF5BinaryTarfiles.pl   | 366 +++
 bin/pkgscrpts/makeInternalREADME.pl   | 215 +++
 bin/pkgscrpts/makeOuterREADME.pl  | 182 ++
 bin/runtest   | 966 ++
 tools/Makefile.am => bin/snapshot_version |  20 +-
 bin/switch_maint_mode |  81 +++
 bin/timekeeper| 129 
 debian/changelog  |   6 +-
 debian/orig-tar.exclude   |   1 +
 debian/orig-tar.sh|  11 +-
 debian/rules  |   4 +-
 debian/watch  |   9 +-
 src/.indent.pro   | 150 +
 src/hdf5-lin.lnt  |  24 +
 src/hdf5-win.lnt  |  39 ++
 src/hdf5.lnt  |  90 +++
 29 files changed, 4240 insertions(+), 80 deletions(-)
 copy config/linux-gnuaout => .autom4te.cfg (77%)
 create mode 100644 .h5chkright.ini
 delete mode 100644 Makefile
 create mode 100644 bin/README
 create mode 100755 bin/bbrelease
 create mode 100755 bin/checkapi
 create mode 100755 bin/checkposix
 create mode 100755 bin/chkconfigure
 create mode 100755 bin/chkcopyright
 copy tools/src/Makefile.am => bin/debug-ohdr (50%)
 mode change 100644 => 100755
 create mode 100755 bin/errors
 create mode 100755 bin/gcov_script
 create mode 100755 bin/pkgscrpts/h5rmflags
 create mode 100755 bin/pkgscrpts/makeHDF5BinaryTarfiles.pl
 create mode 100755 bin/pkgscrpts/makeInternalREADME.pl
 create mode 100755 bin/pkgscrpts/makeOuterREADME.pl
 create mode 100755 bin/runtest
 copy tools/Makefile.am => bin/snapshot_version (67%)
 create mode 100755 bin/switch_maint_mode
 create mode 100755 bin/timekeeper
 create mode 100644 src/.indent.pro
 create mode 100644 src/hdf5-lin.lnt
 create mode 100644 src/hdf5-win.lnt
 create mode 100644 src/hdf5.lnt

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[hdf5] annotated tag debian/1.10.1+docs-1_exp2 created (now 4994b0b)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.1+docs-1_exp2
in repository hdf5.

at  4994b0b   (tag)
   tagging  1b2b2d5c5578a78b136b3ee296d1671b1c091bdf (commit)
  replaces  debian/1.10.1+docs-1_exp1
 tagged by  Gilles Filippini
on  Mon Oct 23 01:16:55 2017 +0200

- Log -
hdf5 Debian release 1.10.1+docs-1~exp2

Gilles Filippini (1):
  libhdf5[-flavor]-101 conflicts / replaces libhdf5[-flavor]-100

---

No new revisions were added by this update.

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[hdf5] 01/01: debian/rules: fix javahelper invocation (closes: #871506)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to annotated tag debian/1.10.0-patch1+docs-3+deb9u1
in repository hdf5.

commit c0020f9883ab84d5f59a91153a5ff3c59458d197
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Aug 13 19:10:20 2017 +0200

debian/rules: fix javahelper invocation (closes: #871506)

Backport of the fix from unstable.
---
 debian/changelog | 6 ++
 debian/rules | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index fce9172..35d8b47 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.0-patch1+docs-3+deb9u1) stretch; urgency=medium
+
+  * debian/rules: fix javahelper invocation (closes: #871506)
+
+ -- Gilles Filippini <p...@debian.org>  Sat, 19 Aug 2017 09:33:00 +0200
+
 hdf5 (1.10.0-patch1+docs-3) unstable; urgency=medium
 
   * Enable openmpi flavor on hppa (closes: #833457)
diff --git a/debian/rules b/debian/rules
index ad84f79..c6dcede 100755
--- a/debian/rules
+++ b/debian/rules
@@ -107,7 +107,7 @@ SERIAL_FLAGS = $(call FLAVOR_FLAGS,serial) 
--enable-threadsafe --enable-cxx
 # No java >= 1.7 on hppa and hurd-i386
 ifeq (,$(filter $(DEB_HOST_ARCH),hppa hurd-i386))
 SERIAL_FLAGS += --enable-java
-DH_HELPERS = --with-javahelper
+DH_HELPERS = --with javahelper
 install_jni := install_jni
 dh_install_java := dh_install_java
 PACKAGES_java := libhdf5-java libhdf5-jni

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[hdf5] annotated tag debian/1.10.1+docs-1_exp1 created (now 425f15f)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.1+docs-1_exp1
in repository hdf5.

at  425f15f   (tag)
   tagging  fe8937923eebb0008c01980d7005165748f3 (commit)
  replaces  debian/1.10.0-patch1+docs-4
 tagged by  Gilles Filippini
on  Sat Oct 7 15:43:22 2017 +0200

- Log -
hdf5 Debian release 1.10.1+docs-1~exp1

Gilles Filippini (13):
  Improve flavor-configure-option.patch
  dh_auto_test for serial flavor
  Prepare import orig of upstream 1.10.1+docs
  New upstream version 1.10.1+docs
  Merge tag 'upstream/1.10.1+docs'
  Refresh patches
  debian/update-symbols-files-soname: fix script to match distinct sonames
  Rename and update the symbols files with the new sonames
  debian/control: update sonames
  Update symbols and version files
  New patch fix-unaligned-accesses.patch
  mv debian/README{,.Debina} + add v1.10.{0,1} compatibility note
  Upload release 1.10.1+docs-1~exp1 to experimental

---

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[hdf5] annotated tag upstream/1.10.1+docs created (now 97f9780)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag upstream/1.10.1+docs
in repository hdf5.

at  97f9780   (tag)
   tagging  173f2a14e355464971e13898a156b2b030ffd453 (commit)
  replaces  upstream/1.10.0-patch1+docs
 tagged by  Gilles Filippini
on  Tue Oct 3 23:51:38 2017 +0200

- Log -
Upstream version 1.10.1+docs

Gilles Filippini (1):
  New upstream version 1.10.1+docs

---

No new revisions were added by this update.

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[hdf5] annotated tag debian/1.10.0-patch1+docs-3+deb9u1 created (now b178bbb)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-3+deb9u1
in repository hdf5.

at  b178bbb   (tag)
   tagging  c0020f9883ab84d5f59a91153a5ff3c59458d197 (commit)
  replaces  debian/1.10.0-patch1+docs-3
 tagged by  Gilles Filippini
on  Sat Aug 19 09:46:08 2017 +0200

- Log -
hdf5 Debian release 1.10.0-patch1+docs-3+deb9u1

Gilles Filippini (1):
  debian/rules: fix javahelper invocation (closes: #871506)

---

This annotated tag includes the following new commits:

   new  c0020f9   debian/rules: fix javahelper invocation (closes: #871506)

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


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[hdf5] branch pristine-tar updated (b0b03b7 -> 6936e34)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch pristine-tar
in repository hdf5.

  from  b0b03b7   pristine-tar data for hdf5_1.10.0-patch1+docs.orig.tar.gz
   new  6936e34   pristine-tar data for hdf5_1.10.1+docs.orig.tar.gz

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 hdf5_1.10.1+docs.orig.tar.gz.delta | Bin 0 -> 148263 bytes
 hdf5_1.10.1+docs.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)
 create mode 100644 hdf5_1.10.1+docs.orig.tar.gz.delta
 create mode 100644 hdf5_1.10.1+docs.orig.tar.gz.id

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[hdf5] 01/01: pristine-tar data for hdf5_1.10.1+docs.orig.tar.gz

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch pristine-tar
in repository hdf5.

commit 6936e3468557ff99ee09520808e717d13f216bcf
Author: Gilles Filippini <p...@debian.org>
Date:   Tue Oct 3 23:51:38 2017 +0200

pristine-tar data for hdf5_1.10.1+docs.orig.tar.gz
---
 hdf5_1.10.1+docs.orig.tar.gz.delta | Bin 0 -> 148263 bytes
 hdf5_1.10.1+docs.orig.tar.gz.id|   1 +
 2 files changed, 1 insertion(+)

diff --git a/hdf5_1.10.1+docs.orig.tar.gz.delta 
b/hdf5_1.10.1+docs.orig.tar.gz.delta
new file mode 100644
index 000..d1ecc8b
Binary files /dev/null and b/hdf5_1.10.1+docs.orig.tar.gz.delta differ
diff --git a/hdf5_1.10.1+docs.orig.tar.gz.id b/hdf5_1.10.1+docs.orig.tar.gz.id
new file mode 100644
index 000..52f5b7b
--- /dev/null
+++ b/hdf5_1.10.1+docs.orig.tar.gz.id
@@ -0,0 +1 @@
+6e1213928bd8607c736ccdbd614c17628567adeb

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[hdf5] 16/17: closes: #855810

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 608c9fbda6ff0a88de95f38b4f125a66e5e6d607
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Dec 17 22:32:57 2017 +0100

closes: #855810

tested on amdahl.debian.org.
---
 debian/changelog | 1 +
 1 file changed, 1 insertion(+)

diff --git a/debian/changelog b/debian/changelog
index bb4fd3d..fc23713 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
 hdf5 (1.10.1+docs-1~exp3) UNRELEASED; urgency=medium
 
   * Disable dh_auto_test on ppc64el (HDFFV-10309)
+  * This upstream release fixes openmpi flavor on arm64 (closes: #855810)
 
  -- Gilles Filippini <p...@debian.org>  Mon, 23 Oct 2017 20:01:47 +0200
 

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[hdf5] 12/17: mv debian/README{, .Debina} + add v1.10.{0, 1} compatibility note

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit a2e24227cb7fb1dfd3f3ef9379ba5219cf6703c8
Author: Gilles Filippini <p...@debian.org>
Date:   Sat Oct 7 14:06:05 2017 +0200

mv debian/README{,.Debina} + add v1.10.{0,1} compatibility note
---
 debian/README| 19 ---
 debian/README.Debian | 32 
 debian/changelog |  2 ++
 3 files changed, 34 insertions(+), 19 deletions(-)

diff --git a/debian/README b/debian/README
deleted file mode 100644
index b23aef1..000
--- a/debian/README
+++ /dev/null
@@ -1,19 +0,0 @@
-HDF5 for Debian

-
-Some general notes for developers: since 1.8 series HDF Group deprecates 
-enabling the thread-safe option for the C library and at the same time
-supporting C++ and Fortran bindings. Those options cannot cohexist for
-safety because non C libraries wrapper are not thread-aware. 
-Debian GNU/Linux still support a C thread-safe library and the alternative
-bindings, but it does not imply that the Debian distributed C++ and Fortran
-are thread-safe. 
-
-For short: DO NOT use C++ or Fortran bindings in multi-thread programs
-witihout providing yourself mutex infrastructure support for every wrapped 
-function. You can use safely only the C binding in a multi-thread environment.
-That was not different in 1.6 series, just the issue was ignored.
-
-Now, you are warned. 
-
- -- Francesco Paolo Lovergine <fran...@debian.org> Fri Jun 19 22:09:25 CEST 
2009
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 000..f874e7c
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,32 @@
+HDF5 for Debian
+===
+
+On thread safety
+
+Some general notes for developers: since 1.8 series HDF Group deprecates 
+enabling the thread-safe option for the C library and at the same time
+supporting high level (HL), C++ and Fortran bindings. Those options cannot
+cohexist for safety because non C libraries wrapper are not thread-aware. 
+Debian GNU/Linux still support a C thread-safe library and the alternative
+bindings, but it does not imply that the Debian distributed high level, C++
+aand Fortranalibraries are thread-safe. 
+
+For short: DO NOT use HL, C++ or Fortran bindings in multi-thread programs
+witihout providing yourself mutex infrastructure support for every wrapped 
+function. You can use safely only the C binding in a multi-thread environment.
+That was not different in 1.6 series, just the issue was ignored.
+
+Now, you are warned. 
+
+ -- Francesco Paolo Lovergine <fran...@debian.org> Fri Jun 19 22:09:25 CEST 
2009
+
+1.10.0 and 1.10.1 compatibility
+---
+From HDF Group newsletter #153:
+HDF5 releases are always backward compatible. In general, they are also
+forward compatible in maintenance releases of a major release. However,
+the HDF5 - 1.10.0 maintenance release will NOT be able to read HDF5 - 1.10.1
+files that contain a metadata cache image. The metadata cache image must be
+removed with the h5clear tool in order for HDF5 - 1.10.0 to read the file.
+
+ -- Gilles Filippini <p...@debian.fr>  Sat, 07 Oct 2017 14:02:39 +0200
diff --git a/debian/changelog b/debian/changelog
index f34cb33..826c36a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,8 @@ hdf5 (1.10.1+docs-1) UNRELEASED; urgency=medium
 Thanks to James Clarke <jrt...@debian.org>
   * Drop patches CVE-2016-433*.patch (fixed upstream)
   * Refresh other patches
+  * Rename debian/README to debian/README.Debian and add note about
+v1.10.0 and 1.10.1 compatibility
 
   * Improve flavor-configure-option.patch to manage -dev packages'
 symlinks and clean-up debian/rules a bit

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[hdf5] 17/17: Priority: replace 'extra' with 'optional'

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit d5f9a090d1d05480f4ae190a2c4e828de1b15c51
Author: Gilles Filippini <p...@debian.org>
Date:   Thu Dec 21 20:02:24 2017 +0100

Priority: replace 'extra' with 'optional'
---
 debian/changelog | 1 +
 debian/control   | 6 --
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index fc23713..df9351c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ hdf5 (1.10.1+docs-1~exp3) UNRELEASED; urgency=medium
 
   * Disable dh_auto_test on ppc64el (HDFFV-10309)
   * This upstream release fixes openmpi flavor on arm64 (closes: #855810)
+  * Priority: replace 'extra' with 'optional'
 
  -- Gilles Filippini <p...@debian.org>  Mon, 23 Oct 2017 20:01:47 +0200
 
diff --git a/debian/control b/debian/control
index cd4be34..9eafe85 100644
--- a/debian/control
+++ b/debian/control
@@ -71,7 +71,6 @@ Description: Hierarchical Data Format 5 (HDF5) - development 
files - serial vers
 
 Package: libhdf5-openmpi-101
 Section: libs
-Priority: extra
 Architecture: any
 Conflicts: libhdf5-openmpi-100
 Replaces: libhdf5-openmpi-100
@@ -88,7 +87,6 @@ Description: Hierarchical Data Format 5 (HDF5) - runtime 
files - OpenMPI version
 
 Package: libhdf5-openmpi-dev
 Section: libdevel
-Priority: extra
 Architecture: any
 Depends: libhdf5-openmpi-101 (= ${binary:Version}), zlib1g-dev, libaec-dev,
  libjpeg-dev, libopenmpi-dev, ${misc:Depends}
@@ -103,7 +101,6 @@ Description: Hierarchical Data Format 5 (HDF5) - 
development files - OpenMPI ver
 
 Package: libhdf5-mpich-101
 Section: libs
-Priority: extra
 Architecture: any
 Conflicts: libhdf5-mpich-100
 Replaces: libhdf5-mpich-100
@@ -121,7 +118,6 @@ Description: Hierarchical Data Format 5 (HDF5) - runtime 
files - MPICH2 version
 
 Package: libhdf5-mpich-dev
 Section: libdevel
-Priority: extra
 Architecture: any
 Depends: libhdf5-mpich-101 (= ${binary:Version}), zlib1g-dev, libaec-dev,
  libjpeg-dev, libmpich-dev, ${misc:Depends}
@@ -137,7 +133,6 @@ Description: Hierarchical Data Format 5 (HDF5) - 
development files - MPICH versi
 
 Package: libhdf5-mpi-dev
 Section: libdevel
-Priority: extra
 # Must be 'Architecture: any' because ${hdf5-mpi-dev} depends on the arch
 Architecture: any
 Depends: ${hdf5-mpi-dev}, mpi-default-dev, ${misc:Depends}
@@ -187,7 +182,6 @@ Description: Hierarchical Data Format 5 (HDF5) - Runtime 
tools
 
 Package: libhdf5-serial-dev
 Section: oldlibs
-Priority: extra
 Architecture: all
 Depends: libhdf5-dev, ${misc:Depends}
 Description: transitional dummy package

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[hdf5] 15/17: Disable dh_auto_test on ppc64el (HDFFV-10309)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 93b3e2e5cbcefd63fdc5d3f1cc3fb34ed3043552
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Dec 17 22:32:11 2017 +0100

Disable dh_auto_test on ppc64el (HDFFV-10309)
---
 debian/changelog |  6 ++
 debian/rules | 12 +---
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 29881d2..bb4fd3d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.1+docs-1~exp3) UNRELEASED; urgency=medium
+
+  * Disable dh_auto_test on ppc64el (HDFFV-10309)
+
+ -- Gilles Filippini <p...@debian.org>  Mon, 23 Oct 2017 20:01:47 +0200
+
 hdf5 (1.10.1+docs-1~exp2) experimental; urgency=medium
 
   * libhdf5[-flavor]-101 conflicts / replaces libhdf5[-flavor]-100
diff --git a/debian/rules b/debian/rules
index cc6d679..61d79c7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -225,8 +225,6 @@ build_%:
 
 override_dh_auto_build-arch: $(foreach flavor,$(FLAVORS),build_$(flavor))
 
-override_dh_auto_test:
-
 install_%: flavor = $(patsubst install_%,%,$@)
 install_%: builddir = $(CURDIR)/debian/build-$(flavor)
 install_%: destdir = $(builddir)/tmpinst
@@ -308,4 +306,12 @@ auto_test_%: builddir = debian/build-$(flavor)
 auto_test_%:
dh_auto_test -B$(builddir)
 
-override_dh_auto_test: auto_test_serial
+# HDFFV-10309 - long double tests fail on ppc64el
+#elmt 107:
+#   src =  00 3f ff ff ff ff ff ff 
18014398509481983
+#   dst =  00 00 00 00 00 00 00 00 43 50 00 00 00 00 00 00  
18014398509481984.00
+#   ans =  bf f0 00 00 00 00 00 00 43 50 00 00 00 00 00 00  
18014398509481983.00
+ifneq (ppc64el,$(DEB_HOST_ARCH))
+auto_test_serial := auto_test_serial
+endif
+override_dh_auto_test: $(auto_test_serial)

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[hdf5] 13/17: Upload release 1.10.1+docs-1~exp1 to experimental

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit fe8937923eebb0008c01980d7005165748f3
Author: Gilles Filippini <p...@debian.org>
Date:   Sat Oct 7 15:15:28 2017 +0200

Upload release 1.10.1+docs-1~exp1 to experimental
---
 debian/changelog | 4 ++--
 debian/rules | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 826c36a..9ae1e6e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-hdf5 (1.10.1+docs-1) UNRELEASED; urgency=medium
+hdf5 (1.10.1+docs-1~exp1) experimental; urgency=medium
 
   * New upstream release
 
@@ -14,7 +14,7 @@ hdf5 (1.10.1+docs-1) UNRELEASED; urgency=medium
 symlinks and clean-up debian/rules a bit
   * Enable dh_auto_test for serial flavor
 
- -- Gilles Filippini <p...@debian.org>  Tue, 03 Oct 2017 23:46:43 +0200
+ -- Gilles Filippini <p...@debian.org>  Sat, 07 Oct 2017 15:14:49 +0200
 
 hdf5 (1.10.0-patch1+docs-4) unstable; urgency=medium
 
diff --git a/debian/rules b/debian/rules
index 400ac7b..cc6d679 100755
--- a/debian/rules
+++ b/debian/rules
@@ -263,7 +263,7 @@ override_dh_install-arch: $(foreach 
flavor,$(FLAVORS),dh_install_$(flavor))
rm -f debian/$(serpackdev)/usr/lib/$(DEB_HOST_MULTIARCH)/libhdf5_java*
 
 override_dh_makeshlibs:
-   DPKG_GENSYMBOLS_CHECK_LEVEL=0 dh_makeshlibs -- -v$(libversion)
+   dh_makeshlibs -- -v$(libversion)
echo "hdf5-mpi-dev=libhdf5-$(DEFAULT_MPI)-dev" >> 
debian/libhdf5-mpi-dev.substvars
 
 override_dh_shlibdeps:

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[hdf5] 07/17: debian/update-symbols-files-soname: fix script to match distinct sonames

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit fad8333a10306fbcb8fc6a5247da1136399dd18d
Author: Gilles Filippini <p...@debian.org>
Date:   Thu Oct 5 21:03:24 2017 +0200

debian/update-symbols-files-soname: fix script to match distinct sonames
---
 debian/rules   |  4 
 debian/update-symbols-files-soname | 25 -
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/debian/rules b/debian/rules
index e18646f..400ac7b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -152,6 +152,10 @@ DEBIAN_OUT := $(shell \
 .SECONDARY: $(DEBIAN_OUT)
 
 
+# Print sonames
+sonames:
+   @$(foreach interface,$(INTERFACES),echo 
"SONAME$(istr)=$(SONAME$(istr))" &&) true
+
 # Informative target
 info: VARIABLES := package pkgversion upstreamversion libversion $(foreach 
interface,$(INTERFACES),SONAME$(istr))
 info: VARIABLES += FLAVORS DH_OPTIONS DEBIAN_OUT
diff --git a/debian/update-symbols-files-soname 
b/debian/update-symbols-files-soname
index 28bd0d4..a63b3ec 100755
--- a/debian/update-symbols-files-soname
+++ b/debian/update-symbols-files-soname
@@ -5,11 +5,26 @@ set -e
 eval "$(debian/rules sonames)"
 
 [ -f "debian/libhdf5-$SONAME.symbols" ] || mv debian/libhdf5-[0-9]*.symbols 
"debian/libhdf5-$SONAME.symbols"
-[ -f "debian/libhdf5-cpp-$SONAME.symbols" ] || mv 
debian/libhdf5-cpp-[0-9]*.symbols "debian/libhdf5-cpp-$SONAME.symbols"
+[ -f "debian/libhdf5-cpp-$SONAME_CXX.symbols" ] || mv 
debian/libhdf5-cpp-[0-9]*.symbols "debian/libhdf5-cpp-$SONAME_CXX.symbols"
 [ -f "debian/libhdf5-openmpi-$SONAME.symbols" ] || mv 
debian/libhdf5-openmpi-[0-9]*.symbols "debian/libhdf5-openmpi-$SONAME.symbols"
 [ -f "debian/libhdf5-mpich-$SONAME.symbols" ] || mv 
debian/libhdf5-mpich-[0-9]*.symbols "debian/libhdf5-mpich-$SONAME.symbols"
 
-sed -ri '/^lib/{s/([\.-])[0-9]+/\1'"$SONAME"'/g}' 
"debian/libhdf5-$SONAME.symbols"
-sed -ri '/^lib/{s/([\.-])[0-9]+/\1'"$SONAME_CXX"'/g}' 
"debian/libhdf5-cpp-$SONAME_CXX.symbols"
-sed -ri '/^lib/{s/([\.-])[0-9]+/\1'"$SONAME"'/g}' 
"debian/libhdf5-openmpi-$SONAME.symbols"
-sed -ri '/^lib/{s/([\.-])[0-9]+/\1'"$SONAME"'/g}' 
"debian/libhdf5-mpich-$SONAME.symbols"
+for flavor in serial openmpi mpich; do
+  if [ $flavor != serial ]; then
+flavor_string="-$flavor"
+  else
+flavor_string=""
+  fi
+  symbols_file=libhdf5${flavor_string}-$SONAME.symbols
+  sed -ri \
+-e "/^libhdf5_${flavor}.so/{s/\.[0-9]+/.$SONAME/;s/-[0-9]+/-$SONAME/}" \
+-e 
"/^libhdf5_${flavor}_fortran.so/{s/\.[0-9]+/.$SONAME_F/;s/-[0-9]+/-$SONAME/}" \
+-e 
"/^libhdf5_${flavor}_hl.so/{s/\.[0-9]+/.$SONAME_HL/;s/-[0-9]+/-$SONAME/}" \
+-e 
"/^libhdf5_${flavor}hl_fortran.so/{s/\.[0-9]+/.$SONAME_HL_F/;s/-[0-9]+/-$SONAME/}"
 \
+debian/$symbols_file
+done
+
+sed -ri \
+  -e "/^libhdf5_cpp.so/{s/\.[0-9]+/.$SONAME_CXX/;s/-[0-9]+/-$SONAME/}" \
+  -e "/^libhdf5_hl_cpp.so/{s/\.[0-9]+/.$SONAME_HL_CXX/;s/-[0-9]+/-$SONAME/}" \
+  debian/libhdf5-cpp-$SONAME_CXX.symbols

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[hdf5] 08/17: Rename and update the symbols files with the new sonames

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 6db84a752b95b85715c9c3489597893c655b99dd
Author: Gilles Filippini <p...@debian.org>
Date:   Thu Oct 5 21:30:54 2017 +0200

Rename and update the symbols files with the new sonames
---
 debian/{libhdf5-100.symbols => libhdf5-101.symbols}   | 8 
 debian/{libhdf5-cpp-100.symbols => libhdf5-cpp-101.symbols}   | 4 ++--
 debian/{libhdf5-mpich-100.symbols => libhdf5-mpich-101.symbols}   | 8 
 .../{libhdf5-openmpi-100.symbols => libhdf5-openmpi-101.symbols}  | 8 
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/debian/libhdf5-100.symbols b/debian/libhdf5-101.symbols
similarity index 99%
rename from debian/libhdf5-100.symbols
rename to debian/libhdf5-101.symbols
index 5c8d3b1..9e613b6 100644
--- a/debian/libhdf5-100.symbols
+++ b/debian/libhdf5-101.symbols
@@ -1,4 +1,4 @@
-libhdf5_serial.so.100 libhdf5-100
+libhdf5_serial.so.101 libhdf5-101
  H5AC_BT2_HDR@HDF5_SERIAL_1.8.7 1.8.13
  H5AC_BT2_INT@HDF5_SERIAL_1.8.7 1.8.13
  H5AC_BT2_LEAF@HDF5_SERIAL_1.8.7 1.8.13
@@ -2926,7 +2926,7 @@ libhdf5_serial.so.100 libhdf5-100
  Nflock@HDF5_SERIAL_1.10.0 1.10.0
  Pflock@HDF5_SERIAL_1.10.0 1.10.0
  epoch_marker_class@HDF5_SERIAL_1.8.7 1.8.13
-libhdf5_serial_fortran.so.100 libhdf5-100
+libhdf5_serial_fortran.so.100 libhdf5-101
  HD5f2cstring@HDF5_SERIAL_1.8.7 1.8.13
  HD5packFstring@HDF5_SERIAL_1.8.7 1.8.13
  HDF5_CPP_1.10.0@HDF5_CPP_1.10.0 1.10.0
@@ -4088,7 +4088,7 @@ libhdf5_serial_fortran.so.100 libhdf5-100
  h5zunregister_c@HDF5_SERIAL_1.10.0 1.10.0
  integer_types_@HDF5_SERIAL_1.8.7 1.8.13
  predefined_types_@HDF5_SERIAL_1.8.7 1.8.13
-libhdf5_serial_hl.so.100 libhdf5-100
+libhdf5_serial_hl.so.100 libhdf5-101
  H5DOappend@HDF5_SERIAL_1.10.0 1.10.0
  H5DOwrite_chunk@HDF5_SERIAL_1.8.11 1.8.13
  H5DSattach_scale@HDF5_SERIAL_1.8.7 1.8.13
@@ -4294,7 +4294,7 @@ libhdf5_serial_hl.so.100 libhdf5-100
  str_cset@HDF5_SERIAL_1.8.7 1.8.13
  str_pad@HDF5_SERIAL_1.8.7 1.8.13
  str_size@HDF5_SERIAL_1.8.7 1.8.13
-libhdf5_serialhl_fortran.so.100 libhdf5-100
+libhdf5_serialhl_fortran.so.100 libhdf5-101
  H5IM_get_palette@HDF5_SERIAL_1.8.7 1.8.13
  H5IMget_palettef@HDF5_SERIAL_1.8.7 1.8.13
  H5IMmake_image_24bitf@HDF5_SERIAL_1.8.7 1.8.13
diff --git a/debian/libhdf5-cpp-100.symbols b/debian/libhdf5-cpp-101.symbols
similarity index 99%
rename from debian/libhdf5-cpp-100.symbols
rename to debian/libhdf5-cpp-101.symbols
index cfdb8b5..eb42f2e 100644
--- a/debian/libhdf5-cpp-100.symbols
+++ b/debian/libhdf5-cpp-101.symbols
@@ -1,4 +1,4 @@
-libhdf5_cpp.so.100 libhdf5-cpp-100 #MINVER#
+libhdf5_cpp.so.101 libhdf5-cpp-101 #MINVER#
  (optional|c++)"H5::AbstractDs::AbstractDs()@HDF5_CPP_1.8.9" 1.8.13
  (optional|c++)"H5::AbstractDs::getArrayType() const@HDF5_CPP_1.8.9" 1.8.13
  (optional|c++)"H5::AbstractDs::getCompType() const@HDF5_CPP_1.8.9" 1.8.13
@@ -1199,7 +1199,7 @@ libhdf5_cpp.so.100 libhdf5-cpp-100 #MINVER#
  (optional|c++)"vtable for H5::ReferenceException@HDF5_CPP_1.8.9" 1.8.13
  (optional|c++)"vtable for H5::StrType@HDF5_CPP_1.8.9" 1.8.13
  (optional|c++)"vtable for H5::VarLenType@HDF5_CPP_1.8.9" 1.8.13
-libhdf5_hl_cpp.so.100 libhdf5-cpp-100 #MINVER#
+libhdf5_hl_cpp.so.100 libhdf5-cpp-101 #MINVER#
  (optional|c++)"FL_PacketTable::AppendPacket(void*)@HDF5_CPP_1.8.9" 1.8.13
  (arch-bits!=64|optional|c++)"FL_PacketTable::AppendPackets(unsigned int, 
void*)@HDF5_CPP_1.10.0" 1.10.0
  (arch-bits=64|optional|c++)"FL_PacketTable::AppendPackets(unsigned long, 
void*)@HDF5_CPP_1.8.13" 1.8.13
diff --git a/debian/libhdf5-mpich-100.symbols b/debian/libhdf5-mpich-101.symbols
similarity index 99%
rename from debian/libhdf5-mpich-100.symbols
rename to debian/libhdf5-mpich-101.symbols
index bcc9e88..68f292f 100644
--- a/debian/libhdf5-mpich-100.symbols
+++ b/debian/libhdf5-mpich-101.symbols
@@ -1,4 +1,4 @@
-libhdf5_mpich.so.100 libhdf5-mpich-100 #MINVER#
+libhdf5_mpich.so.101 libhdf5-mpich-101 #MINVER#
  H5AC_BT2_HDR@HDF5_MPI_1.8.7 1.8.13
  H5AC_BT2_INT@HDF5_MPI_1.8.7 1.8.13
  H5AC_BT2_LEAF@HDF5_MPI_1.8.7 1.8.13
@@ -2972,7 +2972,7 @@ libhdf5_mpich.so.100 libhdf5-mpich-100 #MINVER#
  Nflock@HDF5_MPI_1.10.0 1.10.0
  Pflock@HDF5_MPI_1.10.0 1.10.0
  epoch_marker_class@HDF5_MPI_1.8.7 1.8.13
-libhdf5_mpich_fortran.so.100 libhdf5-mpich-100 #MINVER#
+libhdf5_mpich_fortran.so.100 libhdf5-mpich-101 #MINVER#
  HD5f2cstring@HDF5_MPI_1.8.7 1.8.13
  HD5packFstring@HDF5_MPI_1.8.7 1.8.13
  HDF5_MPI_1.10.0@HDF5_MPI_1.10.0 1.10.0
@@ -4135,7 +4135,7 @@ libhdf5_mpich_fortran.so.100 libhdf5-mpich-100 #MINVER#
  h5zunregister_c@HDF5_MPI_1.10.0 1.10.0
  integer_types_@HDF5_MPI_1.8.7 1.8.13
  predefined_types_@HDF5_MPI_1.8.7 1.8.13
-libhdf5_mpich_hl.so.100 libhdf5-mpich-100 #MINVER#
+libhdf5_mpich_hl.so.100 libhdf5-mpich-101 #MINVER#
  H5DOappend@HDF5_MPI_1.10.0 1.10.0
  H5DOwrite_chu

[hdf5] 06/17: Refresh patches

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit b270aaefbfa7b46e13b80b29a8db2ac5a6d911e6
Author: Gilles Filippini <p...@debian.org>
Date:   Wed Oct 4 19:52:24 2017 +0200

Refresh patches

Drop CVE-2016-433*.patch (fixed upstream).
---
 debian/changelog |   5 +
 debian/patches/CVE-2016-4330.patch   |  20 ---
 debian/patches/CVE-2016-4331-1.patch | 229 ---
 debian/patches/CVE-2016-4331-2.patch |  19 ---
 debian/patches/CVE-2016-4332.patch   |  37 -
 debian/patches/CVE-2016-4333.patch   |  23 ---
 debian/patches/flavor-configure-option.patch | 186 +++---
 debian/patches/java-runtime-exception.patch  |   2 +-
 debian/patches/path_max.diff |  35 +++-
 debian/patches/relax-version-check.patch |  18 +--
 debian/patches/series|   5 -
 debian/patches/ullong_force.diff |   4 +-
 12 files changed, 140 insertions(+), 443 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ba3032b..15e6ef2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,10 @@
 hdf5 (1.10.1+docs-1) UNRELEASED; urgency=medium
 
+  * New upstream release
+
+  * Drop patches CVE-2016-433*.patch (fixed upstream)
+  * Refresh other patches
+
   * Improve flavor-configure-option.patch to manage -dev packages'
 symlinks and clean-up debian/rules a bit
   * Enable dh_auto_test for serial flavor
diff --git a/debian/patches/CVE-2016-4330.patch 
b/debian/patches/CVE-2016-4330.patch
deleted file mode 100644
index cbc09b3..000
--- a/debian/patches/CVE-2016-4330.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-commit b1eb1b3ee8693e2a56b074315b521c66255acca1
-Author: Neil Fortner <nfort...@hdfgroup.org>
-Date:   Thu Sep 1 17:24:24 2016 -0500
-
-Replace assertion in H5O_dtype_decode_helper for number of array 
dimensions with a check and error. The assertion was inappropriate because it 
is operating on data read from the file, which the library does not always have 
direct control of.
-
-diff --git a/src/H5Odtype.c b/src/H5Odtype.c
-index e51d319..eae542b 100644
 a/src/H5Odtype.c
-+++ b/src/H5Odtype.c
-@@ -519,7 +519,8 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned 
*ioflags/*in,out*/, const uint8_t **p
- dt->shared->u.array.ndims = *(*pp)++;
- 
- /* Double-check the number of dimensions */
--HDassert(dt->shared->u.array.ndims <= H5S_MAX_RANK);
-+if(dt->shared->u.array.ndims > H5S_MAX_RANK)
-+HGOTO_ERROR(H5E_DATATYPE, H5E_CANTLOAD, FAIL, "too many 
dimensions for array datatype")
- 
- /* Skip reserved bytes, if version has them */
- if(version < H5O_DTYPE_VERSION_3)
diff --git a/debian/patches/CVE-2016-4331-1.patch 
b/debian/patches/CVE-2016-4331-1.patch
deleted file mode 100644
index 078c982..000
--- a/debian/patches/CVE-2016-4331-1.patch
+++ /dev/null
@@ -1,229 +0,0 @@
-commit 2409f991667283f8fa1dacc66f245950693495aa
-Author: Neil Fortner <nfort...@hdfgroup.org>
-Date:   Thu Sep 8 10:48:54 2016 -0500
-
-Fix issues in H5Znbit.c where the decompression algorithm would not check 
the compressed data for validity, potentially causing a buffer overflow.
-
-Index: hdf5/src/H5Znbit.c
-===
 hdf5.orig/src/H5Znbit.c
-+++ hdf5/src/H5Znbit.c
-@@ -60,11 +60,11 @@ static void H5Z_nbit_decompress_one_noop
-unsigned char *buffer, size_t *j, int *buf_len, 
unsigned size);
- static void H5Z_nbit_decompress_one_atomic(unsigned char *data, size_t 
data_offset,
- unsigned char *buffer, size_t *j, int *buf_len, 
parms_atomic p);
--static void H5Z_nbit_decompress_one_array(unsigned char *data, size_t 
data_offset,
-+static herr_t H5Z__nbit_decompress_one_array(unsigned char *data, size_t 
data_offset,
-unsigned char *buffer, size_t *j, int *buf_len, const unsigned 
parms[]);
--static void H5Z_nbit_decompress_one_compound(unsigned char *data, size_t 
data_offset,
-+static herr_t H5Z__nbit_decompress_one_compound(unsigned char *data, size_t 
data_offset,
-   unsigned char *buffer, size_t *j, int *buf_len, const unsigned 
parms[]);
--static void H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, 
unsigned char *buffer,
-+static herr_t H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, 
unsigned char *buffer,
- const unsigned parms[]);
- static void H5Z_nbit_compress_one_nooptype(unsigned char *data, size_t 
data_offset,
-  unsigned char *buffer, size_t *j, int *buf_len, unsigned 
size);
-@@ -990,7 +990,8 @@ H5Z_filter_nbit(unsigned flags, size_t c
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation 
failed fo

[hdf5] 03/17: Prepare import orig of upstream 1.10.1+docs

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit c93c5c5ab444cb804ffb1e5f244ebe6196069776
Author: Gilles Filippini <p...@debian.org>
Date:   Tue Oct 3 23:47:09 2017 +0200

Prepare import orig of upstream 1.10.1+docs

The HDF Group repositories have moved to git. The HDF5 documentation
repository is now:
  https://bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
---
 debian/changelog   | 4 ++--
 debian/orig-tar.sh | 6 --
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index fd764f4..ba3032b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,10 @@
-hdf5 (1.10.0-patch1+docs-5) UNRELEASED; urgency=medium
+hdf5 (1.10.1+docs-1) UNRELEASED; urgency=medium
 
   * Improve flavor-configure-option.patch to manage -dev packages'
 symlinks and clean-up debian/rules a bit
   * Enable dh_auto_test for serial flavor
 
- -- Gilles Filippini <p...@debian.org>  Fri, 10 Feb 2017 00:26:57 +0100
+ -- Gilles Filippini <p...@debian.org>  Tue, 03 Oct 2017 23:46:43 +0200
 
 hdf5 (1.10.0-patch1+docs-4) unstable; urgency=medium
 
diff --git a/debian/orig-tar.sh b/debian/orig-tar.sh
index 76ffab3..717b526 100755
--- a/debian/orig-tar.sh
+++ b/debian/orig-tar.sh
@@ -2,7 +2,7 @@
 # Called from uscan with parameters:
 # --upstream-version  
 #
-# Require svn
+# Require git
 set -e
 
 UPSTREAM_VERSION="$2"
@@ -22,7 +22,9 @@ HTML_DIR="$DEBIAN_SOURCE_DIR/html"
 tar xf $3
 
 # get docs
-/usr/bin/svn export 
https://svn.hdfgroup.uiuc.edu/hdf5doc/branches/hdf5_"$(echo 
"$UPSTREAM_DOC_VERSION" | sed 's/\./_/g')"/html "$SOURCE_DIR/html"
+git clone --depth 1 --single-branch --branch hdf5_"$(echo 
"$UPSTREAM_DOC_VERSION" | sed 's/\./_/g')" 
https://bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
+mv hdf5doc/html $SOURCE_DIR
+rm -fr hdf5doc
 
 # rename upstream source dir
 # excluding files matched by debian/orig-tar.exclude

-- 
Alioth's /usr/local/bin/git-commit-notice on 
/srv/git.debian.org/git/pkg-grass/hdf5.git

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[hdf5] 01/17: Improve flavor-configure-option.patch

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit d793c46dd5c8c70e90ae2b16d993f40d72168bc6
Author: Gilles Filippini <p...@debian.org>
Date:   Fri Feb 10 16:43:26 2017 +0100

Improve flavor-configure-option.patch

to manage -dev packages' symlinks and clean-up debian/rules a bit.
---
 debian/changelog |   7 +
 debian/libhdf5-flavor-dev.install.in |   9 +-
 debian/libhdf5-flavor-dev.links.in   |  17 --
 debian/man/h5pcc.mpich.1 |   1 +
 debian/man/h5pcc.openmpi.1   |   1 +
 debian/man/h5pfc.mpich.1 |   1 +
 debian/man/h5pfc.openmpi.1   |   1 +
 debian/patches/flavor-configure-option.patch | 235 ++-
 debian/rules |  15 +-
 9 files changed, 217 insertions(+), 70 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 90309cb..dae1364 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+hdf5 (1.10.0-patch1+docs-5) UNRELEASED; urgency=medium
+
+  * Improve flavor-configure-option.patch to manage -dev packages'
+symlinks and clean-up debian/rules a bit
+
+ -- Gilles Filippini <p...@debian.org>  Fri, 10 Feb 2017 00:26:57 +0100
+
 hdf5 (1.10.0-patch1+docs-4) unstable; urgency=medium
 
   * debian/rules: fix javahelper invocation (closes: #871506)
diff --git a/debian/libhdf5-flavor-dev.install.in 
b/debian/libhdf5-flavor-dev.install.in
index 1c1742b..9acd7d4 100644
--- a/debian/libhdf5-flavor-dev.install.in
+++ b/debian/libhdf5-flavor-dev.install.in
@@ -2,5 +2,10 @@ usr/include
 usr/lib/*/libhdf5*.so
 usr/lib/*/libhdf5*.settings
 usr/lib/*/libhdf5*.a
-@IFMPI@usr/bin/h5pcc
-@IFMPI@usr/bin/h5pfc
+usr/lib/*/hdf5/*/libhdf5*.so
+usr/lib/*/hdf5/*/libhdf5*.settings
+usr/lib/*/hdf5/*/libhdf5*.a
+usr/lib/*/hdf5/*/include
+usr/lib/*/hdf5/*/lib
+@IFMPI@usr/bin/h5pcc.@FLAVOR@
+@IFMPI@usr/bin/h5pfc.@FLAVOR@
diff --git a/debian/libhdf5-flavor-dev.links.in 
b/debian/libhdf5-flavor-dev.links.in
deleted file mode 100644
index 4b996c3..000
--- a/debian/libhdf5-flavor-dev.links.in
+++ /dev/null
@@ -1,17 +0,0 @@
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@.so 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5.so
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@_fortran.so 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_fortran.so
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@_hl.so 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_hl.so
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@hl_fortran.so 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5hl_fortran.so
-@IFSERIAL@usr/lib/@MULTIARCH@/libhdf5_cpp.so 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_cpp.so
-@IFSERIAL@usr/lib/@MULTIARCH@/libhdf5_hl_cpp.so 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_hl_cpp.so
-
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@.a 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5.a
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@_fortran.a 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_fortran.a
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@_hl.a 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_hl.a
-usr/lib/@MULTIARCH@/libhdf5@FLAVORLIB@hl_fortran.a 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5hl_fortran.a
-@IFSERIAL@usr/lib/@MULTIARCH@/libhdf5_cpp.a 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_cpp.a
-@IFSERIAL@usr/lib/@MULTIARCH@/libhdf5_hl_cpp.a 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5_hl_cpp.a
-
-usr/include/hdf5/@FLAVOR@ usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/include
-usr/lib/@MULTIARCH@/hdf5/@FLAVOR@ usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/lib
-usr/lib/@MULTIARCH@/libhdf5_@FLAVOR@.settings 
usr/lib/@MULTIARCH@/hdf5/@FLAVOR@/libhdf5.settings
diff --git a/debian/man/h5pcc.mpich.1 b/debian/man/h5pcc.mpich.1
new file mode 12
index 000..ac75158
--- /dev/null
+++ b/debian/man/h5pcc.mpich.1
@@ -0,0 +1 @@
+h5pcc.1
\ No newline at end of file
diff --git a/debian/man/h5pcc.openmpi.1 b/debian/man/h5pcc.openmpi.1
new file mode 12
index 000..ac75158
--- /dev/null
+++ b/debian/man/h5pcc.openmpi.1
@@ -0,0 +1 @@
+h5pcc.1
\ No newline at end of file
diff --git a/debian/man/h5pfc.mpich.1 b/debian/man/h5pfc.mpich.1
new file mode 12
index 000..5b3fd95
--- /dev/null
+++ b/debian/man/h5pfc.mpich.1
@@ -0,0 +1 @@
+h5pfc.1
\ No newline at end of file
diff --git a/debian/man/h5pfc.openmpi.1 b/debian/man/h5pfc.openmpi.1
new file mode 12
index 000..5b3fd95
--- /dev/null
+++ b/debian/man/h5pfc.openmpi.1
@@ -0,0 +1 @@
+h5pfc.1
\ No newline at end of file
diff --git a/debian/patches/flavor-configure-option.patch 
b/debian/patches/flavor-configure-option.patch
index 7fdab33..10f1dcd 100644
--- a/debian/patches/flavor-configure-option.patch
+++ b/debian/patches/flavor-configure-option.patch
@@ -6,11 +6,11 @@ Description: Add option --with-flavor= to 
configure
  * serial is built with no flavor name
  * $mpi parallel versions use --with-flavor=$mpi
 Author: Gilles Filippini <p...@debian.org>
-Index: hdf5/configure.ac
+Index: hdf5-1.10.0-patch1

Bug#638753: libhdf5-serial-1.8.7: threadsafe memory leaks

[Gilles Filippini]

Control: tags -1 + moreinfo

Hi,

On Sun, 21 Aug 2011 17:35:26 +0200 Jerome BENOIT 
wrote:
> Package: libhdf5-serial-1.8.7
> Severity: wishlist
> 
> Hello:
> 
> Since a while I have noticed via valgrind some memory leaks let by the 
> function `H5Zfilter_avail':
> the following Code reproduce the issue:
> 
> --8><---
> // gcc -o test_H5Zfilter_avail test_H5Zfilter_avail.c -lhdf5
> // valgrind --leak-check=yes --leak-check=full --show-reachable=yes 
> ./test_H5Zfilter_avail
> //
> 
> #include 
> #include 
> 
> // http://wiki.hdfgroup.org
> #ifndef H5Z_BZIP2
> #define H5Z_BZIP2 307
> #endif
> 
> int main(int nargs, char *args[]) {
> 
>   fprintf(stderr,
>   "filter with identifier `%d' is %s registered\n",
>   H5Z_BZIP2,
>   (H5Zfilter_avail(H5Z_BZIP2))?"already":"not"
>   );
> 
>   return (0); }
> --><8-
> 
> A closer look shows that the memory leakes are let by the threadsafe 
> machinery.

When trying to reproduce this bug I only get 'still reachable' class
memory leaks, with the very same small memory footprint no matter how
many times H5Zfilter_avail was called. Is that what you experienced?
I tend to consider 'still reachable' memory leaks not leaks. Especially
when there're stable.

Thanks,

_g.



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Bug#879143: pdal: please build-depend on libhdf5-dev instead of transitional package libhdf5-serial-dev

[Gilles Filippini]

Source: pdal
Version: 1.5.0-4
Severity: normal
Control: block 878535 by -1

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Hi,

libhdf5-serial-dev has been a transitional dummy package for at least 3 Debian 
releases.
Please build-depend on libhdf5-dev instead.

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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Bug#875925: hdf5: interaction with nfs changed between jessie and stretch

[Gilles Filippini]

Hi Frédéric,

pi...@synchrotron-soleil.fr a écrit le 16/09/2017 à 07:25 :
> Source: hdf5
> Version: 1.10.0-patch1+docs-3
> Severity: important
> 
> Dear Maintainer,
> 
> after upgrading my system from jessie to stretch, I could not read anymore my 
> hdf5 files located on
> our nfs filesystem.
> 
> I have an error like this 
> 
> Can not flock ...
> 
> looking at the nfs documentation, I could find flock in the local_lock 
> options which is set to
> "none" on my system.
> 
> Since I red that some of these options can create conflict between lock 
> mechanism.
> And because I am not the only one accessing these files (other system are 
> CentOS 5, 6).
> I would like your opinion on the best way to solve this issue.

Well, honestly I'm not at ease at all with file locking over NFS. Would
you mind forwarding this question to upstream [1]?

[1] h...@hdfgroup.org

As I understand it, you should experience the very same problem using
flock(1) shell command on these files. Is that correct?

Thanks,

_g.



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[hdf5] 01/01: debian/rules: fix javahelper invocation (closes: #871506)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit f4b5e675a41b9cc71a093b66781dbb2a4f646061
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Aug 13 19:10:20 2017 +0200

debian/rules: fix javahelper invocation (closes: #871506)
---
 debian/changelog | 6 ++
 debian/rules | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index fce9172..90309cb 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.0-patch1+docs-4) unstable; urgency=medium
+
+  * debian/rules: fix javahelper invocation (closes: #871506)
+
+ -- Gilles Filippini <p...@debian.org>  Sun, 13 Aug 2017 18:50:36 +0200
+
 hdf5 (1.10.0-patch1+docs-3) unstable; urgency=medium
 
   * Enable openmpi flavor on hppa (closes: #833457)
diff --git a/debian/rules b/debian/rules
index ad84f79..c6dcede 100755
--- a/debian/rules
+++ b/debian/rules
@@ -107,7 +107,7 @@ SERIAL_FLAGS = $(call FLAVOR_FLAGS,serial) 
--enable-threadsafe --enable-cxx
 # No java >= 1.7 on hppa and hurd-i386
 ifeq (,$(filter $(DEB_HOST_ARCH),hppa hurd-i386))
 SERIAL_FLAGS += --enable-java
-DH_HELPERS = --with-javahelper
+DH_HELPERS = --with javahelper
 install_jni := install_jni
 dh_install_java := dh_install_java
 PACKAGES_java := libhdf5-java libhdf5-jni

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[hdf5] annotated tag debian/1.10.0-patch1+docs-4 created (now dcd6f44)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-4
in repository hdf5.

at  dcd6f44   (tag)
   tagging  f4b5e675a41b9cc71a093b66781dbb2a4f646061 (commit)
  replaces  debian/1.10.0-patch1+docs-3
 tagged by  Gilles Filippini
on  Sun Aug 13 19:15:28 2017 +0200

- Log -
hdf5 Debian release 1.10.0-patch1+docs-4

Gilles Filippini (1):
  debian/rules: fix javahelper invocation (closes: #871506)

---

No new revisions were added by this update.

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[hdf5] branch master updated (d0f0356 -> f4b5e67)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master
in repository hdf5.

  from  d0f0356   Upload release 1.10.0-patch1+docs-3 to unstable
   new  f4b5e67   debian/rules: fix javahelper invocation (closes: #871506)

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 6 ++
 debian/rules | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

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Bug#855810: libhdf5-openmpi-100 doesn't work on arm64

[Gilles Filippini]

Package: libhdf5-openmpi-100
Version: 1.10.0-patch1+docs-3
Severity: important

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

The attached simple testcase fails on arm64 with:
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) MPI-process 0:
  #000: ../../../src/H5F.c line 491 in H5Fcreate(): unable to create file
major: File accessibilty
minor: Unable to open file
  #001: ../../../src/H5Fint.c line 1100 in H5F_open(): unable to open
file: time = Mon Feb 20 10:57:13 2017
, name = 'test.med', tent_flags = 13
major: File accessibilty
minor: Unable to open file
  #002: ../../../src/H5FD.c line 812 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
  #003: ../../../src/H5FDmpio.c line 997 in H5FD_mpio_open():
MPI_File_open failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
  #004: ../../../src/H5FDmpio.c line 997 in H5FD_mpio_open():
MPI_ERR_OTHER: known error not in list
major: Internal error (too specific to document in detail)
minor: MPI Error String
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) MPI-process 0:
  #000: ../../../src/H5F.c line 749 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type

To build it:
$ h5pcc.openmpi -o h5_mpitest h5_mpitest.c

To run it:
$ OMPI_MCA_orte_rsh_agent=/bin/false mpirun.openmpi -np 1 ./h5_mpitest

_g.

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=a4uN
-END PGP SIGNATURE-
#include 
#include 
#define FILE "test.med"

int main(int argc, char *argv[]) {

   hid_t   file_id;
   hid_t   fapl;
   int mpi_size, mpi_rank, ret=0;

   MPI_Init(, );
   MPI_Comm_size(MPI_COMM_WORLD, _size);
   MPI_Comm_rank(MPI_COMM_WORLD, _rank);

   /* Create a new file using default properties. */
   fapl = H5Pcreate (H5P_FILE_ACCESS);
   H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);
   file_id = H5Fcreate(FILE,H5F_ACC_TRUNC, H5P_DEFAULT,fapl);

   /* Close the file. */
   H5Fclose(file_id);
   H5Pclose(fapl);

   MPI_Finalize();
   return 0;
}

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[hdf5] 03/03: Upload release 1.10.0-patch1+docs-3 to unstable

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit d0f0356cc5da09be9d339c46ea01d7296c0a07b8
Author: Gilles Filippini <p...@debian.org>
Date:   Mon Dec 5 09:28:08 2016 +0100

Upload release 1.10.0-patch1+docs-3 to unstable
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 2f4cf49..fce9172 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,9 @@
-hdf5 (1.10.0-patch1+docs-3) UNRELEASED; urgency=medium
+hdf5 (1.10.0-patch1+docs-3) unstable; urgency=medium
 
   * Enable openmpi flavor on hppa (closes: #833457)
   * Fix missing symbols for powerpcspe 'closes: #842595)
 
- -- Gilles Filippini <p...@debian.org>  Sun, 04 Dec 2016 14:58:27 +0100
+ -- Gilles Filippini <p...@debian.org>  Mon, 05 Dec 2016 09:27:39 +0100
 
 hdf5 (1.10.0-patch1+docs-2) unstable; urgency=medium
 

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[hdf5] 01/03: Enable openmpi flavor on hppa

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 84c3691d27e6073cf8158591e26a771337e4ebd6
Author: Gilles Filippini <p...@debian.org>
Date:   Mon Dec 5 09:26:44 2016 +0100

Enable openmpi flavor on hppa
---
 debian/changelog | 6 ++
 debian/rules | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 06271e9..9086b46 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.0-patch1+docs-3) UNRELEASED; urgency=medium
+
+  * Enable openmpi flavor on hppa (closes: #833457)
+
+ -- Gilles Filippini <p...@debian.org>  Sun, 04 Dec 2016 14:58:27 +0100
+
 hdf5 (1.10.0-patch1+docs-2) unstable; urgency=medium
 
   * Don't build the java wrapper library on hppa and hurd-i386 where
diff --git a/debian/rules b/debian/rules
index 6122b04..ad84f79 100755
--- a/debian/rules
+++ b/debian/rules
@@ -60,8 +60,8 @@ DEFAULT_MPI=$(ARCH_DEFAULT_MPI_IMPL)
 # Setting empty OMPIARCHS and MPICHARCHS environment variables disables
 # the related mpi targets
 #
-# openmpi broken on archs hppa m68k sh4 (2016-02-24)
-OMPIARCHS?=any !hppa !m68k !sh4
+# openmpi broken on archs m68k sh4 (2016-12-04)
+OMPIARCHS?=any !m68k !sh4
 MPICHARCHS?=any
 
 # BEGIN - Construct the FLAVORS list for current arch

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[hdf5] 02/03: Fix missing symbols for powerpcspe

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 46ad5837f27f14bf96f611bd7e38db22b447aa9a
Author: Gilles Filippini <p...@debian.org>
Date:   Mon Dec 5 09:27:27 2016 +0100

Fix missing symbols for powerpcspe
---
 debian/changelog   | 1 +
 debian/libhdf5-100.symbols | 6 +++---
 debian/libhdf5-mpich-100.symbols   | 6 +++---
 debian/libhdf5-openmpi-100.symbols | 6 +++---
 4 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9086b46..2f4cf49 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
 hdf5 (1.10.0-patch1+docs-3) UNRELEASED; urgency=medium
 
   * Enable openmpi flavor on hppa (closes: #833457)
+  * Fix missing symbols for powerpcspe 'closes: #842595)
 
  -- Gilles Filippini <p...@debian.org>  Sun, 04 Dec 2016 14:58:27 +0100
 
diff --git a/debian/libhdf5-100.symbols b/debian/libhdf5-100.symbols
index d0ead73..5c8d3b1 100644
--- a/debian/libhdf5-100.symbols
+++ b/debian/libhdf5-100.symbols
@@ -2454,19 +2454,19 @@ libhdf5_serial.so.100 libhdf5-100
  H5T__conv_ldouble_double@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_float@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_int@HDF5_SERIAL_1.8.7 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_ldouble_llong@HDF5_SERIAL_1.8.7 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_ldouble_llong@HDF5_SERIAL_1.8.7 
1.8.13
  H5T__conv_ldouble_long@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_schar@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_short@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_uchar@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_uint@HDF5_SERIAL_1.8.7 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_ldouble_ullong@HDF5_SERIAL_1.8.7 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_ldouble_ullong@HDF5_SERIAL_1.8.7 
1.8.13
  H5T__conv_ldouble_ulong@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_ldouble_ushort@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_llong_double@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_llong_float@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_llong_int@HDF5_SERIAL_1.8.7 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_llong_ldouble@HDF5_SERIAL_1.8.7 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_llong_ldouble@HDF5_SERIAL_1.8.7 
1.8.13
  H5T__conv_llong_long@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_llong_schar@HDF5_SERIAL_1.8.7 1.8.13
  H5T__conv_llong_short@HDF5_SERIAL_1.8.7 1.8.13
diff --git a/debian/libhdf5-mpich-100.symbols b/debian/libhdf5-mpich-100.symbols
index bbf3d6f..bcc9e88 100644
--- a/debian/libhdf5-mpich-100.symbols
+++ b/debian/libhdf5-mpich-100.symbols
@@ -2509,19 +2509,19 @@ libhdf5_mpich.so.100 libhdf5-mpich-100 #MINVER#
  H5T__conv_ldouble_double@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_float@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_int@HDF5_MPI_1.8.10 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_ldouble_llong@HDF5_MPI_1.8.10 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_ldouble_llong@HDF5_MPI_1.8.10 
1.8.13
  H5T__conv_ldouble_long@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_schar@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_short@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_uchar@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_uint@HDF5_MPI_1.8.10 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_ldouble_ullong@HDF5_MPI_1.8.10 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_ldouble_ullong@HDF5_MPI_1.8.10 
1.8.13
  H5T__conv_ldouble_ulong@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_ushort@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_llong_double@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_llong_float@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_llong_int@HDF5_MPI_1.8.10 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_llong_ldouble@HDF5_MPI_1.8.10 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_llong_ldouble@HDF5_MPI_1.8.10 
1.8.13
  H5T__conv_llong_long@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_llong_schar@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_llong_short@HDF5_MPI_1.8.10 1.8.13
diff --git a/debian/libhdf5-openmpi-100.symbols 
b/debian/libhdf5-openmpi-100.symbols
index 4cb91a5..be8c8be 100644
--- a/debian/libhdf5-openmpi-100.symbols
+++ b/debian/libhdf5-openmpi-100.symbols
@@ -2509,19 +2509,19 @@ libhdf5_openmpi.so.100 libhdf5-openmpi-100 #MINVER#
  H5T__conv_ldouble_double@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_float@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_int@HDF5_MPI_1.8.10 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_ldouble_llong@HDF5_MPI_1.8.10 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_ldouble_llong@HDF5_MPI_1.8.10 
1.8.13
  H5T__conv_ldouble_long@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_schar@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_short@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_uchar@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_uint@HDF5_MPI_1.8.10 1.8.13
- (arch=!powerpc !ppc64)H5T__conv_ldouble_ullong@HDF5_MPI_1.8.10 1.8.13
+ (arch=!powerpc !powerpcspe !ppc64)H5T__conv_ldouble_ullong@HDF5_MPI_1.8.10 
1.8.13
  H5T__conv_ldouble_ulong@HDF5_MPI_1.8.10 1.8.13
  H5T__conv_ldouble_ushort@HDF5_MPI_1

[hdf5] annotated tag debian/1.10.0-patch1+docs-3 created (now 902295c)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-3
in repository hdf5.

at  902295c   (tag)
   tagging  d0f0356cc5da09be9d339c46ea01d7296c0a07b8 (commit)
  replaces  debian/1.10.0-patch1+docs-2
 tagged by  Gilles Filippini
on  Mon Dec 5 09:41:20 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-3

Gilles Filippini (3):
  Enable openmpi flavor on hppa
  Fix missing symbols for powerpcspe
  Upload release 1.10.0-patch1+docs-3 to unstable

---

No new revisions were added by this update.

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[hdf5] branch master updated (a1028b8 -> d0f0356)

[Gilles Filippini]

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pini pushed a change to branch master
in repository hdf5.

  from  a1028b8   Upload release 1.10.0-patch1+docs-2 to unstable
   new  84c3691   Enable openmpi flavor on hppa
   new  46ad583   Fix missing symbols for powerpcspe
   new  d0f0356   Upload release 1.10.0-patch1+docs-3 to unstable

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Summary of changes:
 debian/changelog   | 7 +++
 debian/libhdf5-100.symbols | 6 +++---
 debian/libhdf5-mpich-100.symbols   | 6 +++---
 debian/libhdf5-openmpi-100.symbols | 6 +++---
 debian/rules   | 4 ++--
 5 files changed, 18 insertions(+), 11 deletions(-)

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Bug#846353: FTBFS: ERROR: Test "ruby2.3" failed. Exiting.

[Gilles Filippini]

Sebastiaan Couwenberg a écrit le 03/12/2016 à 19:33 :
> Control: tags -1 pending
> 
> On 12/03/2016 07:19 PM, Gilles Filippini wrote:
>> I've filed #846853 against src:hdf-eos5. There are issues in
>> ruby-hdfeos5 as well. See the attached patch.
>>
>> With these fixes the ruby-hdfeos5 testsuite passes on 64 bit and 32 bit
>> arches.
> 
> Thanks for the patch! I've applied it in git, and will do a team upload
> after hdf-eos5 is fixed, unless Youhei beats me to it.

Fixed hdf-eos5 is now in unstable.

Thanks,

_g.




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[hdf5] branch experimental deleted (was 23a1d22)

[Gilles Filippini]

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   was  23a1d22   debian/changelog update

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[hdf5] branch master-1.10 deleted (was a1028b8)

[Gilles Filippini]

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pini pushed a change to branch master-1.10
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   was  a1028b8   Upload release 1.10.0-patch1+docs-2 to unstable

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[hdf5] branch svn-import/upstream deleted (was 6e36993)

[Gilles Filippini]

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   was  6e36993   [svn-upgrade] Tagging new upstream version, hdf5 (1.6.7)

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  discards  6e36993   [svn-upgrade] Tagging new upstream version, hdf5 (1.6.7)
  discards  5236969   [svn-upgrade] Integrating new upstream version, hdf5 
(1.6.7)
  discards  1adcfae   [svn-upgrade] Tagging new upstream version, hdf5 (1.6.6)
  discards  7fc1a99   [svn-upgrade] Integrating new upstream version, hdf5 
(1.6.6)
  discards  2b0bc25   [svn-inject] Tagging upstream source version of hdf5
  discards  ac6c743   [svn-inject] Installing original source of hdf5

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[hdf5] branch svn-import/1.6.6 deleted (was 61c2cc5)

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   was  61c2cc5   Fixating a minor bug

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  discards  61c2cc5   Fixating a minor bug
  discards  4dee1e9   Creating branch
  discards  d19531f   Missing 1.6.6-4 tag added

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[hdf5] branch svn-import/trunk@813 deleted (was 73fc22c)

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   was  73fc22c   [svn-inject] Installing original source of hdf5

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[hdf5] branch svn-import/1.6.5 deleted (was c995159)

[Gilles Filippini]

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   was  c995159   Main fixes for current sid branch

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  discards  c995159   Main fixes for current sid branch
  discards  55a2edd   Fixing RC bug in branch
  discards  f9232bc   Branching 1.6.5
  discards  d12a15b   [svn-buildpackage] Tagging hdf5 (1.6.5-5)

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[hdf5] annotated tag debian/1.10.0-patch1+docs-2_exp2 created (now d18594c)

[Gilles Filippini]

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in repository hdf5.

at  d18594c   (tag)
   tagging  2b023745ecbbca3fa13bda41da0ee6ee6525cbfb (commit)
  replaces  debian/1.10.0-patch1+docs-2_exp1
 tagged by  Gilles Filippini
on  Thu Dec 1 22:06:56 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-2~exp2

Gilles Filippini (1):
  Fix FTBFS on kfreebsd-*

---

No new revisions were added by this update.

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[hdf5] annotated tag debian/1.10.0-patch1+docs-2 created (now d364296)

[Gilles Filippini]

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pini pushed a change to annotated tag debian/1.10.0-patch1+docs-2
in repository hdf5.

at  d364296   (tag)
   tagging  a1028b874cf7b427335bcac1d8b12b2d779de884 (commit)
  replaces  debian/1.10.0-patch1+docs-2_exp2
 tagged by  Gilles Filippini
on  Sun Dec 4 14:14:32 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-2

Gilles Filippini (2):
  No java wrapper library on hppa and hurd-i386
  Upload release 1.10.0-patch1+docs-2 to unstable

---

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[hdf5] 01/03: Fix FTBFS on kfreebsd-*

[Gilles Filippini]

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pini pushed a commit to branch master
in repository hdf5.

commit 2b023745ecbbca3fa13bda41da0ee6ee6525cbfb
Author: Gilles Filippini <p...@debian.org>
Date:   Thu Dec 1 21:53:53 2016 +0100

Fix FTBFS on kfreebsd-*
---
 debian/changelog | 6 ++
 debian/rules | 5 +
 2 files changed, 11 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index f3a0df6..d73bb84 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.0-patch1+docs-2~exp2) experimental; urgency=medium
+
+  * Fix FTBFS on kfreebsd-*
+
+ -- Gilles Filippini <p...@debian.org>  Thu, 01 Dec 2016 21:52:43 +0100
+
 hdf5 (1.10.0-patch1+docs-2~exp1) experimental; urgency=medium
 
   * New binary packages for the java wrapper library which is now
diff --git a/debian/rules b/debian/rules
index 9a758a5..edafea7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -111,6 +111,11 @@ MPI_ENV = 
H5_LDFLAGS="-Wl,--version-script,\$$(top_srcdir)/debian/map_mpi.ver" \
CC=mpicc.$(1) FC=mpif90.$(1) F9X=mpif90.$(1) 
RUNPARALLEL=/usr/bin/mpirun.$(1)
 OPENMPI_ENV := $(call MPI_ENV,openmpi)
 MPICH_ENV := $(call MPI_ENV,mpich)
+
+# Fix FTBFS on kfreebsd-*
+ifneq (,$(filter $(DEB_HOST_ARCH),kfreebsd-i386 kfreebsd-amd64))
+SERIAL_ENV += H5_CPPFLAGS="-I/usr/lib/jvm/default-java/include/bsd"
+endif
 # END - Configure flags and environment variables
 
 # Compose the packages' name flavor part from $(flavor)

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[hdf5] 03/03: Upload release 1.10.0-patch1+docs-2 to unstable

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit a1028b874cf7b427335bcac1d8b12b2d779de884
Author: Gilles Filippini <p...@debian.org>
Date:   Sun Dec 4 13:55:37 2016 +0100

Upload release 1.10.0-patch1+docs-2 to unstable
---
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index c1783f2..06271e9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-hdf5 (1.10.0-patch1+docs-2~exp3) experimental; urgency=medium
+hdf5 (1.10.0-patch1+docs-2) unstable; urgency=medium
 
   * Don't build the java wrapper library on hppa and hurd-i386 where
 there is no JDK >= 1.7

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[hdf5] branch master updated (d8e4794 -> a1028b8)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master
in repository hdf5.

  from  d8e4794   Merge branch 'master-1.10'
  adds  9e3c930   New binary packages libhdf5-java and libhdf5-jni
  adds  a45e5ce   java: new patch java-runtime-exception.patch
  adds  c209863   Fix building arch all only
  adds  b8880c0   Upload release 1.10.0-patch1+docs-2~exp1 to experimental
   new  2b02374   Fix FTBFS on kfreebsd-*
   new  794c4a2   No java wrapper library on hppa and hurd-i386
   new  a1028b8   Upload release 1.10.0-patch1+docs-2 to unstable

The 3 revisions listed above as "new" are entirely new to this
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Summary of changes:
 debian/changelog| 22 +++
 debian/control  | 22 ++-
 debian/control.in   | 22 ++-
 debian/libhdf5-doc.doc-base |  2 +-
 debian/libhdf5-java.jlibs   |  1 +
 debian/libhdf5-jni.install.in   |  1 +
 debian/patches/java-runtime-exception.patch | 13 +++
 debian/patches/series   |  1 +
 debian/rules| 57 -
 9 files changed, 128 insertions(+), 13 deletions(-)
 create mode 100644 debian/libhdf5-java.jlibs
 create mode 100644 debian/libhdf5-jni.install.in
 create mode 100644 debian/patches/java-runtime-exception.patch

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[hdf5] 02/03: No java wrapper library on hppa and hurd-i386

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit 794c4a2b25b213c2fda6c73bb4bfb3d3091a3a2d
Author: Gilles Filippini <p...@debian.org>
Date:   Fri Dec 2 11:35:11 2016 +0100

No java wrapper library on hppa and hurd-i386

where there is no JDK >= 1.7.
---
 debian/changelog  |  7 +++
 debian/control|  2 +-
 debian/control.in |  2 +-
 debian/rules  | 32 
 4 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d73bb84..c1783f2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+hdf5 (1.10.0-patch1+docs-2~exp3) experimental; urgency=medium
+
+  * Don't build the java wrapper library on hppa and hurd-i386 where
+there is no JDK >= 1.7
+
+ -- Gilles Filippini <p...@debian.org>  Fri, 02 Dec 2016 11:32:12 +0100
+
 hdf5 (1.10.0-patch1+docs-2~exp2) experimental; urgency=medium
 
   * Fix FTBFS on kfreebsd-*
diff --git a/debian/control b/debian/control
index 6ca1eb8..7ac035a 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 10~), mpi-default-dev, 
libmpich-dev, zlib1g-dev,
  libjpeg-dev, gfortran,
  sharutils, chrpath, autotools-dev, automake, dh-autoreconf,
  libaec-dev,
- default-jdk-headless, javahelper,
+ default-jdk-headless (>= 2:1.7) [!hppa !hurd-i386], javahelper [!hppa 
!hurd-i386],
 Build-Depends-Indep:
  doxygen, php-cli,
 Standards-Version: 3.9.8
diff --git a/debian/control.in b/debian/control.in
index 6585f19..595c05b 100644
--- a/debian/control.in
+++ b/debian/control.in
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 10~), mpi-default-dev, 
libmpich-dev, zlib1g-dev,
  libjpeg-dev, gfortran,
  sharutils, chrpath, autotools-dev, automake, dh-autoreconf,
  libaec-dev,
- default-jdk-headless, javahelper,
+ default-jdk-headless (>= 2:1.7) [!hppa !hurd-i386], javahelper [!hppa 
!hurd-i386],
 Build-Depends-Indep:
  doxygen, php-cli,
 Standards-Version: 3.9.8
diff --git a/debian/rules b/debian/rules
index edafea7..6122b04 100755
--- a/debian/rules
+++ b/debian/rules
@@ -102,7 +102,19 @@ CONFIGURE_FLAGS = --prefix=/usr 
--host=$(DEB_HOST_GNU_TYPE) \
  --with-szlib \
  --enable-fortran --enable-fortran2003
 FLAVOR_FLAGS = --includedir=\$${prefix}/include/hdf5/$(1) --with-flavor=$(1)
-SERIAL_FLAGS = $(call FLAVOR_FLAGS,serial) --enable-threadsafe --enable-cxx 
--enable-java
+SERIAL_FLAGS = $(call FLAVOR_FLAGS,serial) --enable-threadsafe --enable-cxx
+
+# No java >= 1.7 on hppa and hurd-i386
+ifeq (,$(filter $(DEB_HOST_ARCH),hppa hurd-i386))
+SERIAL_FLAGS += --enable-java
+DH_HELPERS = --with-javahelper
+install_jni := install_jni
+dh_install_java := dh_install_java
+PACKAGES_java := libhdf5-java libhdf5-jni
+else
+export DH_OPTIONS += -Nlibhdf5-java -Nlibhdf5-jni
+endif
+
 OPENMPI_FLAGS = $(call FLAVOR_FLAGS,openmpi) --enable-parallel=yes
 MPICH_FLAGS = $(call FLAVOR_FLAGS,mpich) --enable-parallel=yes
 
@@ -182,7 +194,7 @@ $(foreach flavor,$(FLAVORS),$(eval $(call 
helper_flavor_rule,$(flavor),$(flavorp
 
 
 %:
-   dh $@ --with javahelper
+   dh $@ $(DH_HELPERS)
 
 override_dh_auto_clean: debian/control
rm -fr $(DEBIAN_OUT)
@@ -225,15 +237,17 @@ install_%:
dh_auto_install --builddirectory=$(builddir) --destdir=$(destdir)
chrpath -d $(destdir)/usr/lib/*/libhdf5*so*
 
-override_dh_auto_install-arch: serial_builddir = $(CURDIR)/debian/build-serial
-override_dh_auto_install-arch: serial_destdir = $(serial_builddir)/tmpinst
-override_dh_auto_install-arch: $(foreach flavor,$(FLAVORS),install_$(flavor))
+install_jni: serial_builddir = $(CURDIR)/debian/build-serial
+install_jni: serial_destdir = $(serial_builddir)/tmpinst
+install_jni: install_serial
dh_auto_install --builddirectory=$(serial_builddir)/java/src/jni 
--destdir=$(serial_destdir)
jnilib=$(serial_destdir)/usr/lib/$(DEB_HOST_MULTIARCH)/libhdf5_java.so 
&& \
install -D 
$(serial_destdir)/usr/lib/$(DEB_HOST_MULTIARCH)/libhdf5_java.so \

$(serial_destdir)/usr/lib/$(DEB_HOST_MULTIARCH)/jni/libhdf5_java.so
 
-PACKAGES_serial := $(serpack) $(package)-dev hdf5-helpers hdf5-tools 
$(sercpppack) libhdf5-java libhdf5-jni
+override_dh_auto_install-arch: $(foreach flavor,$(FLAVORS),install_$(flavor)) 
$(install_jni)
+
+PACKAGES_serial := $(serpack) $(package)-dev hdf5-helpers hdf5-tools 
$(sercpppack) $(PACKAGES_java)
 PACKAGES_openmpi := $(openmpipack) $(package)-openmpi-dev
 PACKAGES_mpich := $(mpichpack) $(package)-mpich-dev
 
@@ -285,9 +299,11 @@ dh_install_doc:
  -execdir /bin/sh -c "/usr/bin/php -f '{}' > '{}.new'" \; \
  -exec mv "{}.new" "{}" \;
 
-override_dh_auto_build-indep: build_doc build_serial
-override_dh_auto_install-indep:
+dh_install_java: build_serial
mv debian/build-serial/java/sr

[hdf5] branch master-1.10 updated (b8880c0 -> a1028b8)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master-1.10
in repository hdf5.

  from  b8880c0   Upload release 1.10.0-patch1+docs-2~exp1 to experimental
   new  2b02374   Fix FTBFS on kfreebsd-*
   new  794c4a2   No java wrapper library on hppa and hurd-i386
   new  a1028b8   Upload release 1.10.0-patch1+docs-2 to unstable

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog  | 13 +
 debian/control|  2 +-
 debian/control.in |  2 +-
 debian/rules  | 37 +
 4 files changed, 44 insertions(+), 10 deletions(-)

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Bug#846353: FTBFS: ERROR: Test "ruby2.3" failed. Exiting.

[Gilles Filippini]

Control: block -1 by 846853
Control: tags -1 + patch

Gilles Filippini a écrit le 03/12/2016 à 02:34 :
> Gilles Filippini a écrit le 03/12/2016 à 01:35 :
>> Gilles Filippini a écrit le 02/12/2016 à 23:26 :
>>> Sebastiaan Couwenberg a écrit le 02/12/2016 à 15:34 :
>>>> On 12/02/2016 09:55 AM, Sebastiaan Couwenberg wrote:
>>>>> On 12/01/2016 07:48 PM, Sebastiaan Couwenberg wrote:
>>>>>> On Wed, 30 Nov 2016 15:10:03 + Iain Lane wrote:
>>>>>>> This package FTBFS on 32 bit arches (works on amd64 and other 64 bit
>>>>>>> arches), maybe due to the new hdf5
>>>>>>
>>>>>> Quite likely, since hdf-eos5 hasn't been rebuilt for the hdf5 transition
>>>>>> yet. I suspect this issue to fix itself once that's done.
>>>>>
>>>>> It did not, but did only fail on 32-bit architectures.
>>>>
>>>> Gilles, these failures seem to be caused by the hid_t type change from
>>>> 32-bit to a 64-bit value. I'm not sure how to fix it for ruby-hdfeos5,
>>>> can you maybe provide a patch?
>>>
>>> Damn, I tested the build on amd64 only :/
>>> I've tried fixing the 'incompatible pointer type' warning, but it
>>> deosn't change anything wrt the test suite.
>>> Is there a way to ensure first that hdf-eos5 works fine on 32 bit archs?
>>
>> CC-ing Alastair, maintainer of hdf-eos5.
>>
>> AIUI the problem lies in hdf-eos5. I've ran a very simple C test made
>> after the first lines of test/test_gd.rb (source attached), both on
>> amd64 and i386. It succeeds on amd64 and fails on i386 at the
>> HE5_GDdetach step with:
>>
>> $ ./myhe5-32
>> bufsize = 19
>> ColumnAmountAerosol
>> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>>   #000: GDapi.c line 1140 in HE5_GDchkgdid(): Cannot get the Grid index
>>
>> major: Invalid arguments to routine
>> minor: Out of range
>> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>>   #000: EHapi.c line 2206 in HE5_EHchkfid(): Invalid file ID: 0. ID
>> should range from 67108864 to  67109064 .
>>
>> major: Invalid arguments to routine
>> minor: Bad value
>> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>>   #000: GDapi.c line 1151 in HE5_GDchkgdid(): Checking for file ID failed.
>>
>> major: Invalid arguments to routine
>> minor: Out of range
>> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>>   #000: GDapi.c line 12623 in HE5_GDdetach(): Checking for grid ID failed.
>>
>> major: Invalid arguments to routine
>> minor: Out of range
> 
> The problem seems to be the type conversion functions in EHapi.c. For
> instance:
> 
> long
> HE5_EHhid2long(hid_t invalue)
> {
>   long  outvalue = FAIL;
> 
>   if (sizeof(hid_t) == sizeof(int))
> outvalue = HE5_EHint2long(invalue);
>   else if (sizeof(hid_t) == sizeof(long))
> outvalue = invalue;
> 
>   return(outvalue);
> }
> 
> On 32 bit archs:
>   sizeof(hid_t) != sizeof(int)
>   sizeof(hid_t) != sizeof(long)
>   sizeof(hid_t) == sizeof(long long)
> 
> The conversion functions should be adapted accordingly.

I've filed #846853 against src:hdf-eos5. There are issues in
ruby-hdfeos5 as well. See the attached patch.

With these fixes the ruby-hdfeos5 testsuite passes on 64 bit and 32 bit
arches.

Thanks,

_g.
diff -Nru ruby-hdfeos5-1.2/debian/changelog ruby-hdfeos5-1.2/debian/changelog
--- ruby-hdfeos5-1.2/debian/changelog   2016-03-01 10:16:48.0 +0100
+++ ruby-hdfeos5-1.2/debian/changelog   2016-12-03 18:55:27.0 +0100
@@ -1,3 +1,10 @@
+ruby-hdfeos5 (1.2-6.1) unstable; urgency=medium
+
+  * Non-maintainer upload
+  * Fix FTBFS on 32 bi architectures against hdf5 1.10 (closes: #846353)
+
+ -- Gilles Filippini <p...@debian.org>  Sat, 03 Dec 2016 18:55:27 +0100
+
 ruby-hdfeos5 (1.2-6) unstable; urgency=medium
 
   * Remove dbg package
diff -Nru ruby-hdfeos5-1.2/debian/patches/hid_t.patch 
ruby-hdfeos5-1.2/debian/patches/hid_t.patch
--- ruby-hdfeos5-1.2/debian/patches/hid_t.patch 1970-01-01 01:00:00.0 
+0100
+++ ruby-hdfeos5-1.2/debian/patches/hid_t.patch 2016-12-03 15:23:32.0 
+0100
@@ -0,0 +1,142 @@
+Index: ruby-hdfeos5-1.2/hdfeos5gd_wrap.c
+===
+--- ruby-hdfeos5-1.2.orig/hdfeos5gd_wrap.c
 ruby-hdfeos5-1.2/hdfeos5gd_wrap.c
+@@ -20,7 +20,7 @@
+ #endif
+ 
+ extern int   check_numbertype(char *);
+-extern int   change_numbertype(char *);
++extern hid_t change_numbertype(char *);
+ extern int   change_entryc

Bug#846353: FTBFS: ERROR: Test "ruby2.3" failed. Exiting.

[Gilles Filippini]

Gilles Filippini a écrit le 03/12/2016 à 01:35 :
> Gilles Filippini a écrit le 02/12/2016 à 23:26 :
>> Sebastiaan Couwenberg a écrit le 02/12/2016 à 15:34 :
>>> On 12/02/2016 09:55 AM, Sebastiaan Couwenberg wrote:
>>>> On 12/01/2016 07:48 PM, Sebastiaan Couwenberg wrote:
>>>>> On Wed, 30 Nov 2016 15:10:03 + Iain Lane wrote:
>>>>>> This package FTBFS on 32 bit arches (works on amd64 and other 64 bit
>>>>>> arches), maybe due to the new hdf5
>>>>>
>>>>> Quite likely, since hdf-eos5 hasn't been rebuilt for the hdf5 transition
>>>>> yet. I suspect this issue to fix itself once that's done.
>>>>
>>>> It did not, but did only fail on 32-bit architectures.
>>>
>>> Gilles, these failures seem to be caused by the hid_t type change from
>>> 32-bit to a 64-bit value. I'm not sure how to fix it for ruby-hdfeos5,
>>> can you maybe provide a patch?
>>
>> Damn, I tested the build on amd64 only :/
>> I've tried fixing the 'incompatible pointer type' warning, but it
>> deosn't change anything wrt the test suite.
>> Is there a way to ensure first that hdf-eos5 works fine on 32 bit archs?
> 
> CC-ing Alastair, maintainer of hdf-eos5.
> 
> AIUI the problem lies in hdf-eos5. I've ran a very simple C test made
> after the first lines of test/test_gd.rb (source attached), both on
> amd64 and i386. It succeeds on amd64 and fails on i386 at the
> HE5_GDdetach step with:
> 
> $ ./myhe5-32
> bufsize = 19
> ColumnAmountAerosol
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>   #000: GDapi.c line 1140 in HE5_GDchkgdid(): Cannot get the Grid index
> 
> major: Invalid arguments to routine
> minor: Out of range
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>   #000: EHapi.c line 2206 in HE5_EHchkfid(): Invalid file ID: 0. ID
> should range from 67108864 to  67109064 .
> 
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>   #000: GDapi.c line 1151 in HE5_GDchkgdid(): Checking for file ID failed.
> 
> major: Invalid arguments to routine
> minor: Out of range
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
>   #000: GDapi.c line 12623 in HE5_GDdetach(): Checking for grid ID failed.
> 
> major: Invalid arguments to routine
> minor: Out of range

The problem seems to be the type conversion functions in EHapi.c. For
instance:

long
HE5_EHhid2long(hid_t invalue)
{
  long  outvalue = FAIL;

  if (sizeof(hid_t) == sizeof(int))
outvalue = HE5_EHint2long(invalue);
  else if (sizeof(hid_t) == sizeof(long))
outvalue = invalue;

  return(outvalue);
}

On 32 bit archs:
  sizeof(hid_t) != sizeof(int)
  sizeof(hid_t) != sizeof(long)
  sizeof(hid_t) == sizeof(long long)

The conversion functions should be adapted accordingly.

Thanks,

_g.



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Bug#846353: FTBFS: ERROR: Test "ruby2.3" failed. Exiting.

[Gilles Filippini]

Gilles Filippini a écrit le 02/12/2016 à 23:26 :
> Sebastiaan Couwenberg a écrit le 02/12/2016 à 15:34 :
>> On 12/02/2016 09:55 AM, Sebastiaan Couwenberg wrote:
>>> On 12/01/2016 07:48 PM, Sebastiaan Couwenberg wrote:
>>>> On Wed, 30 Nov 2016 15:10:03 + Iain Lane wrote:
>>>>> This package FTBFS on 32 bit arches (works on amd64 and other 64 bit
>>>>> arches), maybe due to the new hdf5
>>>>
>>>> Quite likely, since hdf-eos5 hasn't been rebuilt for the hdf5 transition
>>>> yet. I suspect this issue to fix itself once that's done.
>>>
>>> It did not, but did only fail on 32-bit architectures.
>>
>> Gilles, these failures seem to be caused by the hid_t type change from
>> 32-bit to a 64-bit value. I'm not sure how to fix it for ruby-hdfeos5,
>> can you maybe provide a patch?
> 
> Damn, I tested the build on amd64 only :/
> I've tried fixing the 'incompatible pointer type' warning, but it
> deosn't change anything wrt the test suite.
> Is there a way to ensure first that hdf-eos5 works fine on 32 bit archs?

CC-ing Alastair, maintainer of hdf-eos5.

AIUI the problem lies in hdf-eos5. I've ran a very simple C test made
after the first lines of test/test_gd.rb (source attached), both on
amd64 and i386. It succeeds on amd64 and fails on i386 at the
HE5_GDdetach step with:

$ ./myhe5-32
bufsize = 19
ColumnAmountAerosol
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
  #000: GDapi.c line 1140 in HE5_GDchkgdid(): Cannot get the Grid index

major: Invalid arguments to routine
minor: Out of range
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
  #000: EHapi.c line 2206 in HE5_EHchkfid(): Invalid file ID: 0. ID
should range from 67108864 to  67109064 .

major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
  #000: GDapi.c line 1151 in HE5_GDchkgdid(): Checking for file ID failed.

major: Invalid arguments to routine
minor: Out of range
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 4142823168:
  #000: GDapi.c line 12623 in HE5_GDdetach(): Checking for grid ID failed.

major: Invalid arguments to routine
minor: Out of range

Thanks,

_g.
#include 

const char *filename = "OMI-Aura_L3-OMAEROe_2008m0101_v003-2009m0114t114202.he5";

int main(int argc, char *argv[]) {
  hid_t fid, gdid;
  long ngrid, bufsize = 0;
  herr_t ret;
  char *buffer;
  fid = HE5_EHopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
  ngrid = HE5_GDinqgrid(filename, NULL, );
  printf("bufsize = %ld\n", bufsize);
  buffer = malloc((size_t)bufsize+1);
  buffer[bufsize] = '\0';
  ngrid = HE5_GDinqgrid(filename, buffer, );
  printf("%s\n", buffer);

  gdid = HE5_GDattach(fid, buffer);
  HE5_GDdetach(gdid);
  free(buffer);
  ret = HE5_EHclose(fid);
  return ret;
}


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Bug#846353: FTBFS: ERROR: Test "ruby2.3" failed. Exiting.

[Gilles Filippini]

Sebastiaan Couwenberg a écrit le 02/12/2016 à 15:34 :
> On 12/02/2016 09:55 AM, Sebastiaan Couwenberg wrote:
>> On 12/01/2016 07:48 PM, Sebastiaan Couwenberg wrote:
>>> On Wed, 30 Nov 2016 15:10:03 + Iain Lane wrote:
 This package FTBFS on 32 bit arches (works on amd64 and other 64 bit
 arches), maybe due to the new hdf5
>>>
>>> Quite likely, since hdf-eos5 hasn't been rebuilt for the hdf5 transition
>>> yet. I suspect this issue to fix itself once that's done.
>>
>> It did not, but did only fail on 32-bit architectures.
> 
> Gilles, these failures seem to be caused by the hid_t type change from
> 32-bit to a 64-bit value. I'm not sure how to fix it for ruby-hdfeos5,
> can you maybe provide a patch?

Damn, I tested the build on amd64 only :/
I've tried fixing the 'incompatible pointer type' warning, but it
deosn't change anything wrt the test suite.
Is there a way to ensure first that hdf-eos5 works fine on 32 bit archs?

Thanks,

_g.




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[hdf5] annotated tag debian/1.8.13+docs-15+deb8u1 created (now e8d54d6)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.8.13+docs-15+deb8u1
in repository hdf5.

at  e8d54d6   (tag)
   tagging  f29ea1b4f89d3fe035c84c41783be662872b533b (commit)
  replaces  debian/1.8.13+docs-15
 tagged by  Gilles Filippini
on  Tue Nov 29 09:21:28 2016 +0100

- Log -
hdf5 Debian release 1.8.13+docs-15+deb8u1

Gilles Filippini (1):
  Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 CVE-2016-4333

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[hdf5] annotated tag debian/1.10.0-patch1+docs-2_exp1 created (now 5b83ada)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-2_exp1
in repository hdf5.

at  5b83ada   (tag)
   tagging  b8880c0ef93b640bb05178867228070d46f02c92 (commit)
  replaces  debian/1.10.0-patch1+docs-1
 tagged by  Gilles Filippini
on  Tue Nov 29 00:44:19 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-2~exp1

Gilles Filippini (9):
  debian/watch: use dirversionmangle
  Build-Depends: php-cli for php7.0 transition
  Upload release 1.8.16+docs-8 to unstable
  Merge tag 'debian/1.10.0-patch1+docs-1_exp4'
  Merge branch 'master-1.10'
  New binary packages libhdf5-java and libhdf5-jni
  java: new patch java-runtime-exception.patch
  Fix building arch all only
  Upload release 1.10.0-patch1+docs-2~exp1 to experimental

---

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[hdf5] 04/04: Upload release 1.10.0-patch1+docs-2~exp1 to experimental

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit b8880c0ef93b640bb05178867228070d46f02c92
Author: Gilles Filippini <p...@debian.org>
Date:   Tue Nov 29 00:39:42 2016 +0100

Upload release 1.10.0-patch1+docs-2~exp1 to experimental
---
 debian/changelog | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 3999065..f3a0df6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,7 +5,7 @@ hdf5 (1.10.0-patch1+docs-2~exp1) experimental; urgency=medium
   * New patch java-runtime-exception.patch to define HDF5Exception as
 a subclass of RuntimeException, to make it an unchecked exception
 
- -- Gilles Filippini <p...@debian.org>  Thu, 03 Nov 2016 20:37:50 +0100
+ -- Gilles Filippini <p...@debian.org>  Tue, 29 Nov 2016 00:38:20 +0100
 
 hdf5 (1.10.0-patch1+docs-1) unstable; urgency=medium
 

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[hdf5] 03/04: Fix building arch all only

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit c209863620d36b3e943ea9f0dc1e8292cab6fe0f
Author: Gilles Filippini <p...@debian.org>
Date:   Tue Nov 29 00:38:51 2016 +0100

Fix building arch all only
---
 debian/rules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/debian/rules b/debian/rules
index 13d3522..9a758a5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -280,7 +280,7 @@ dh_install_doc:
  -execdir /bin/sh -c "/usr/bin/php -f '{}' > '{}.new'" \; \
  -exec mv "{}.new" "{}" \;
 
-override_dh_auto_build-indep: build_doc
+override_dh_auto_build-indep: build_doc build_serial
 override_dh_auto_install-indep:
mv debian/build-serial/java/src/jarhdf5-$(upstreamversion).jar 
debian/build-serial/java/src/jarhdf5.jar
 override_dh_install-indep: dh_install_serial dh_install_doc

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[hdf5] 01/04: New binary packages libhdf5-java and libhdf5-jni

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit 9e3c9302e5b1f0da377bbb69848d97d09cf944ec
Author: Gilles Filippini <p...@debian.org>
Date:   Thu Nov 3 20:38:12 2016 +0100

New binary packages libhdf5-java and libhdf5-jni
---
 debian/changelog  |  7 +++
 debian/control| 22 +-
 debian/control.in | 22 +-
 debian/libhdf5-doc.doc-base   |  2 +-
 debian/libhdf5-java.jlibs |  1 +
 debian/libhdf5-jni.install.in |  1 +
 debian/rules  | 36 ++--
 7 files changed, 78 insertions(+), 13 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 72cec6f..b87be5f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+hdf5 (1.10.0-patch1+docs-2~exp1) experimental; urgency=medium
+
+  * New binary packages for the java wrapper library which is now
+integrated into the HDF5 source tree: libhdf5-java and libhdf5-jni
+
+ -- Gilles Filippini <p...@debian.org>  Thu, 03 Nov 2016 20:37:50 +0100
+
 hdf5 (1.10.0-patch1+docs-1) unstable; urgency=medium
 
   * Upload to unstable
diff --git a/debian/control b/debian/control
index 5bf9143..6ca1eb8 100644
--- a/debian/control
+++ b/debian/control
@@ -4,10 +4,11 @@ Priority: optional
 Maintainer: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
 Uploaders: Francesco Paolo Lovergine <fran...@debian.org>,
  Gilles Filippini <p...@debian.org>
-Build-Depends: debhelper (>= 9~), mpi-default-dev, libmpich-dev, zlib1g-dev,
+Build-Depends: debhelper (>= 10~), mpi-default-dev, libmpich-dev, zlib1g-dev,
  libjpeg-dev, gfortran,
  sharutils, chrpath, autotools-dev, automake, dh-autoreconf,
  libaec-dev,
+ default-jdk-headless, javahelper,
 Build-Depends-Indep:
  doxygen, php-cli,
 Standards-Version: 3.9.8
@@ -184,3 +185,22 @@ Depends: libhdf5-dev, ${misc:Depends}
 Description: transitional dummy package
  This package is a transitionnal package from libhdf5-serial-dev to
  libhdf5-dev. It can safely be removed.
+
+Package: libhdf5-java
+Section: java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, libhdf5-jni
+Description: Hierarchical Data Format 5 (HDF5) - Java Wrapper Library
+ HDF5 is a file format and library for storing scientific data.
+ HDF5 was designed and implemented to address the deficiencies of
+ HDF4.x. It has a more powerful and flexible data model, supports
+ files larger than 2 GB, and supports parallel I/O.
+ .
+ This package contains the java wrapper library for HDF5.
+
+Package: libhdf5-jni
+Architecture: any
+Multi-Arch: same
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: native library used by libhdf5-java
+ This package is only useful with libhdf5-java.
diff --git a/debian/control.in b/debian/control.in
index a0e8cba..6585f19 100644
--- a/debian/control.in
+++ b/debian/control.in
@@ -4,10 +4,11 @@ Priority: optional
 Maintainer: Debian GIS Project <pkg-grass-devel@lists.alioth.debian.org>
 Uploaders: Francesco Paolo Lovergine <fran...@debian.org>,
  Gilles Filippini <p...@debian.org>
-Build-Depends: debhelper (>= 9~), mpi-default-dev, libmpich-dev, zlib1g-dev,
+Build-Depends: debhelper (>= 10~), mpi-default-dev, libmpich-dev, zlib1g-dev,
  libjpeg-dev, gfortran,
  sharutils, chrpath, autotools-dev, automake, dh-autoreconf,
  libaec-dev,
+ default-jdk-headless, javahelper,
 Build-Depends-Indep:
  doxygen, php-cli,
 Standards-Version: 3.9.8
@@ -184,3 +185,22 @@ Depends: libhdf5-dev, ${misc:Depends}
 Description: transitional dummy package
  This package is a transitionnal package from libhdf5-serial-dev to
  libhdf5-dev. It can safely be removed.
+
+Package: libhdf5-java
+Section: java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, libhdf5-jni
+Description: Hierarchical Data Format 5 (HDF5) - Java Wrapper Library
+ HDF5 is a file format and library for storing scientific data.
+ HDF5 was designed and implemented to address the deficiencies of
+ HDF4.x. It has a more powerful and flexible data model, supports
+ files larger than 2 GB, and supports parallel I/O.
+ .
+ This package contains the java wrapper library for HDF5.
+
+Package: libhdf5-jni
+Architecture: any
+Multi-Arch: same
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: native library used by libhdf5-java
+ This package is only useful with libhdf5-java.
diff --git a/debian/libhdf5-doc.doc-base b/debian/libhdf5-doc.doc-base
index 3635b23..52463c7 100644
--- a/debian/libhdf5-doc.doc-base
+++ b/debian/libhdf5-doc.doc-base
@@ -1,7 +1,7 @@
 Document: libhdf5
 Title: HDF5 manual
 Author: National Center for Supercomputing Applications (NCSA)
-Abstract: Hierachical Data Format 5 (HDF5) - Documentation
+Abstract: Hierarchical Data Format 5 (HDF5) - Documentation
  HDF5 is a file format and library for 

[hdf5] branch jessie created (now f29ea1b)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch jessie
in repository hdf5.

at  f29ea1b   Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 
CVE-2016-4333

This branch includes the following new commits:

   new  f29ea1b   Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 
CVE-2016-4333

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


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[hdf5] 02/04: java: new patch java-runtime-exception.patch

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit a45e5cefde4b3ed9b09ecad6f7811bb5097a1d0c
Author: Gilles Filippini <p...@debian.org>
Date:   Thu Nov 24 23:16:20 2016 +0100

java: new patch java-runtime-exception.patch

Define HDF5Exeption as unchecked (subclass of RuntimeException).
---
 debian/changelog|  2 ++
 debian/patches/java-runtime-exception.patch | 13 +
 debian/patches/series   |  1 +
 3 files changed, 16 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index b87be5f..3999065 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,8 @@ hdf5 (1.10.0-patch1+docs-2~exp1) experimental; urgency=medium
 
   * New binary packages for the java wrapper library which is now
 integrated into the HDF5 source tree: libhdf5-java and libhdf5-jni
+  * New patch java-runtime-exception.patch to define HDF5Exception as
+a subclass of RuntimeException, to make it an unchecked exception
 
  -- Gilles Filippini <p...@debian.org>  Thu, 03 Nov 2016 20:37:50 +0100
 
diff --git a/debian/patches/java-runtime-exception.patch 
b/debian/patches/java-runtime-exception.patch
new file mode 100644
index 000..e0c9972
--- /dev/null
+++ b/debian/patches/java-runtime-exception.patch
@@ -0,0 +1,13 @@
+Index: hdf5/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
+===
+--- hdf5.orig/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
 hdf5/java/src/hdf/hdf5lib/exceptions/HDF5Exception.java
+@@ -32,7 +32,7 @@ package hdf.hdf5lib.exceptions;
+  * error code returned by the HDF5 library.
+  *
+  */
+-public class HDF5Exception extends Exception {
++public class HDF5Exception extends RuntimeException {
+ protected String detailMessage;
+ 
+ /**
diff --git a/debian/patches/series b/debian/patches/series
index ec125b1..bd5dc24 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ CVE-2016-4331-1.patch
 CVE-2016-4331-2.patch
 CVE-2016-4332.patch
 CVE-2016-4333.patch
+java-runtime-exception.patch

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[hdf5] 01/01: Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 CVE-2016-4333

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch jessie
in repository hdf5.

commit f29ea1b4f89d3fe035c84c41783be662872b533b
Author: Gilles Filippini <p...@debian.org>
Date:   Fri Nov 25 18:17:06 2016 +0100

Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 CVE-2016-4333

Backport patches CVE-2016-433*.patch from master-1.10 branch.
---
 debian/changelog |   8 ++
 debian/patches/CVE-2016-4330.patch   |  20 +++
 debian/patches/CVE-2016-4331-1.patch | 229 +++
 debian/patches/CVE-2016-4331-2.patch |  19 +++
 debian/patches/CVE-2016-4332.patch   |  37 ++
 debian/patches/CVE-2016-4333.patch   |  23 
 debian/patches/series|   5 +
 7 files changed, 341 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 98e9952..9789b3f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+hdf5 (1.8.13+docs-15+deb8u1) jessie-security; urgency=high
+
+  * New patches CVE-2016-433*.patch from upstream develop branch
+to fix four vulnerabilities unveiled by TALOS (closes: #845301,
+CVE-2016-4330, CVE-2016-4331, CVE-2016-4332, CVE-2016-4333)
+
+ -- Gilles Filippini <p...@debian.org>  Fri, 25 Nov 2016 00:59:06 +0100
+
 hdf5 (1.8.13+docs-15) unstable; urgency=medium
 
   * New patch HDFFV-8917.patch from upstream to fix a resource
diff --git a/debian/patches/CVE-2016-4330.patch 
b/debian/patches/CVE-2016-4330.patch
new file mode 100644
index 000..8a49ae9
--- /dev/null
+++ b/debian/patches/CVE-2016-4330.patch
@@ -0,0 +1,20 @@
+commit b1eb1b3ee8693e2a56b074315b521c66255acca1
+Author: Neil Fortner <nfort...@hdfgroup.org>
+Date:   Thu Sep 1 17:24:24 2016 -0500
+
+Replace assertion in H5O_dtype_decode_helper for number of array 
dimensions with a check and error. The assertion was inappropriate because it 
is operating on data read from the file, which the library does not always have 
direct control of.
+
+Index: hdf5/src/H5Odtype.c
+===
+--- hdf5.orig/src/H5Odtype.c
 hdf5/src/H5Odtype.c
+@@ -518,7 +518,8 @@ H5O_dtype_decode_helper(H5F_t *f, unsign
+ dt->shared->u.array.ndims = *(*pp)++;
+ 
+ /* Double-check the number of dimensions */
+-HDassert(dt->shared->u.array.ndims <= H5S_MAX_RANK);
++if(dt->shared->u.array.ndims > H5S_MAX_RANK)
++HGOTO_ERROR(H5E_DATATYPE, H5E_CANTLOAD, FAIL, "too many 
dimensions for array datatype")
+ 
+ /* Skip reserved bytes, if version has them */
+ if(version < H5O_DTYPE_VERSION_3)
diff --git a/debian/patches/CVE-2016-4331-1.patch 
b/debian/patches/CVE-2016-4331-1.patch
new file mode 100644
index 000..9d5f487
--- /dev/null
+++ b/debian/patches/CVE-2016-4331-1.patch
@@ -0,0 +1,229 @@
+commit 2409f991667283f8fa1dacc66f245950693495aa
+Author: Neil Fortner <nfort...@hdfgroup.org>
+Date:   Thu Sep 8 10:48:54 2016 -0500
+
+Fix issues in H5Znbit.c where the decompression algorithm would not check 
the compressed data for validity, potentially causing a buffer overflow.
+
+Index: hdf5/src/H5Znbit.c
+===
+--- hdf5.orig/src/H5Znbit.c
 hdf5/src/H5Znbit.c
+@@ -62,11 +62,11 @@ static void H5Z_nbit_decompress_one_noop
+unsigned char *buffer, size_t *j, int *buf_len, 
unsigned size);
+ static void H5Z_nbit_decompress_one_atomic(unsigned char *data, size_t 
data_offset,
+ unsigned char *buffer, size_t *j, int *buf_len, 
parms_atomic p);
+-static void H5Z_nbit_decompress_one_array(unsigned char *data, size_t 
data_offset,
++static herr_t H5Z__nbit_decompress_one_array(unsigned char *data, size_t 
data_offset,
+unsigned char *buffer, size_t *j, int *buf_len, const unsigned 
parms[]);
+-static void H5Z_nbit_decompress_one_compound(unsigned char *data, size_t 
data_offset,
++static herr_t H5Z__nbit_decompress_one_compound(unsigned char *data, size_t 
data_offset,
+   unsigned char *buffer, size_t *j, int *buf_len, const unsigned 
parms[]);
+-static void H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, 
unsigned char *buffer,
++static herr_t H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, 
unsigned char *buffer,
+ const unsigned parms[]);
+ static void H5Z_nbit_compress_one_nooptype(unsigned char *data, size_t 
data_offset,
+  unsigned char *buffer, size_t *j, int *buf_len, unsigned 
size);
+@@ -899,7 +899,8 @@ H5Z_filter_nbit(unsigned flags, size_t c
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation 
failed for nbit decompression")
+ 
+ /* decompress the buffer */
+-H5Z_nbit_decompress(outbuf, d_nelmts, (unsigned char *)*buf, 
cd_values);
++if(H5Z__n

[hdf5] branch master-1.10 updated (d8e4794 -> b8880c0)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master-1.10
in repository hdf5.

  from  d8e4794   Merge branch 'master-1.10'
   new  9e3c930   New binary packages libhdf5-java and libhdf5-jni
   new  a45e5ce   java: new patch java-runtime-exception.patch
   new  c209863   Fix building arch all only
   new  b8880c0   Upload release 1.10.0-patch1+docs-2~exp1 to experimental

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog|  9 +++
 debian/control  | 22 -
 debian/control.in   | 22 -
 debian/libhdf5-doc.doc-base |  2 +-
 debian/libhdf5-java.jlibs   |  1 +
 debian/libhdf5-jni.install.in   |  1 +
 debian/patches/java-runtime-exception.patch | 13 ++
 debian/patches/series   |  1 +
 debian/rules| 38 -
 9 files changed, 95 insertions(+), 14 deletions(-)
 create mode 100644 debian/libhdf5-java.jlibs
 create mode 100644 debian/libhdf5-jni.install.in
 create mode 100644 debian/patches/java-runtime-exception.patch

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[hdf5] branch master-1.10 updated (d07eb80 -> d8e4794)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master-1.10
in repository hdf5.

  from  d07eb80   Upload release 1.10.0-patch1+docs-1 to unstable
  adds  c64a634   debian/watch: use dirversionmangle
  adds  e2896cf   Build-Depends: php-cli for php7.0 transition
  adds  39f9405   Upload release 1.8.16+docs-8 to unstable
  adds  5eb9ff6   Merge tag 'debian/1.10.0-patch1+docs-1_exp4'
  adds  d8e4794   Merge branch 'master-1.10'

No new revisions were added by this update.

Summary of changes:
 debian/changelog | 8 
 1 file changed, 8 insertions(+)

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[hdf5] annotated tag debian/1.10.0-patch1+docs-1 created (now 45ac089)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-1
in repository hdf5.

at  45ac089   (tag)
   tagging  d07eb80e10f7e72233f2a532a7de6c2d0f76637f (commit)
  replaces  debian/1.10.0-patch1+docs-1_exp6
 tagged by  Gilles Filippini
on  Mon Nov 28 09:14:37 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-1

Gilles Filippini (1):
  Upload release 1.10.0-patch1+docs-1 to unstable

---

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[hdf5] 02/02: Merge branch 'master-1.10'

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit d8e47945fcc4cdcc6bc407d5268ef9c0bb755b2e
Merge: 5eb9ff6 d07eb80
Author: Gilles Filippini <p...@debian.org>
Date:   Mon Nov 28 15:42:15 2016 +0100

Merge branch 'master-1.10'

 debian/changelog | 106 +---
 debian/patches/CVE-2016-4330.patch   |  20 +++
 debian/patches/CVE-2016-4331-1.patch | 229 +++
 debian/patches/CVE-2016-4331-2.patch |  19 +++
 debian/patches/CVE-2016-4332.patch   |  37 ++
 debian/patches/CVE-2016-4333.patch   |  23 
 debian/patches/series|   5 +
 debian/rules |   3 +-
 8 files changed, 421 insertions(+), 21 deletions(-)

diff --cc debian/changelog
index 8ec4285,2ec27ec..72cec6f
--- a/debian/changelog
+++ b/debian/changelog
@@@ -13,38 -94,15 +94,23 @@@ hdf5 (1.10.0+docs-1~exp1) experimental
* Refresh other patches
* libhdf5-cpp-: drop versioned dependency on libhdf5-
  to ease future transitions
-   * debian/control.in:
- - Use Build-Depends-Indep
- - Drop - now - useless versioned Build-Depends on dpkg-dev
- - Drop *-dbg packages, superseded by automatic debug packages
- - Standars-Version: bump to 3.9.8 (no changes)
* debian/rules:
- - Migrate to dh with compat=10
  - improve soname retrieval
- - Drop flag OMPI_MCA_disable_memory_allocator (old workaround for
-   bug #531522)
  - replace deprecated '--enable-production' with '--enable-build-mode'
- - Move setting of substvar ${hdf5-mpi-dev} into dh_makeshlib; it was
-   ignored when set at configure step
- - Set default plugins dir to /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/plugins
-   (closes: #826522)
* debian/watch: use dirversionmangle to have upstream releases properly
  sorted
-   * Symbols files:
- - Update from new release
- - Temporarily set DPKG_GENSYMBOLS_CHECK_LEVEL=0
- - Fix arch specific symbols
+   * Bump Standards-Version to 3.9.7 (no change)
  
-  -- Gilles Filippini <p...@debian.org>  Sat, 05 Nov 2016 23:23:33 +0100
+  -- Gilles Filippini <p...@debian.org>  Sat, 16 Apr 2016 09:24:06 +0200
  
 +hdf5 (1.8.16+docs-8) unstable; urgency=medium
 +
 +  * Build-Depends: php-cli instead of php5-cli (closes: #821678)
 +  * debian/watch: use dirversionmangle to have upstream versions
 +properly sorted
 +
 + -- Gilles Filippini <p...@debian.org>  Sat, 23 Apr 2016 11:43:31 +0200
 +
  hdf5 (1.8.16+docs-7) unstable; urgency=medium
  
* debian/rules: fix typo preventing doc installation.

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[hdf5] branch master-1.10 updated (6bf983c -> d07eb80)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master-1.10
in repository hdf5.

  from  6bf983c   Fix FTBFS when building arch-all only
   new  d07eb80   Upload release 1.10.0-patch1+docs-1 to unstable

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listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

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[hdf5] 01/02: Upload release 1.10.0-patch1+docs-1 to unstable

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master
in repository hdf5.

commit d07eb80e10f7e72233f2a532a7de6c2d0f76637f
Author: Gilles Filippini <p...@debian.org>
Date:   Mon Nov 28 09:01:43 2016 +0100

Upload release 1.10.0-patch1+docs-1 to unstable

'Go ahead' received for the transition.
---
 debian/changelog | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 8c2d303..2ec27ec 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.0-patch1+docs-1) unstable; urgency=medium
+
+  * Upload to unstable
+
+ -- Gilles Filippini <p...@debian.org>  Mon, 28 Nov 2016 09:01:23 +0100
+
 hdf5 (1.10.0-patch1+docs-1~exp6) experimental; urgency=medium
 
   * Fix FTBFS when building arch-all only

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[hdf5] branch master updated (5eb9ff6 -> d8e4794)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master
in repository hdf5.

  from  5eb9ff6   Merge tag 'debian/1.10.0-patch1+docs-1_exp4'
  adds  df59eb7   Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 
CVE-2016-4333
  adds  6bf983c   Fix FTBFS when building arch-all only
   new  d07eb80   Upload release 1.10.0-patch1+docs-1 to unstable
   new  d8e4794   Merge branch 'master-1.10'

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog | 106 +---
 debian/patches/CVE-2016-4330.patch   |  20 +++
 debian/patches/CVE-2016-4331-1.patch | 229 +++
 debian/patches/CVE-2016-4331-2.patch |  19 +++
 debian/patches/CVE-2016-4332.patch   |  37 ++
 debian/patches/CVE-2016-4333.patch   |  23 
 debian/patches/series|   5 +
 debian/rules |   3 +-
 8 files changed, 421 insertions(+), 21 deletions(-)
 create mode 100644 debian/patches/CVE-2016-4330.patch
 create mode 100644 debian/patches/CVE-2016-4331-1.patch
 create mode 100644 debian/patches/CVE-2016-4331-2.patch
 create mode 100644 debian/patches/CVE-2016-4332.patch
 create mode 100644 debian/patches/CVE-2016-4333.patch

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[hdf5] annotated tag debian/1.10.0-patch1+docs-1_exp6 created (now 713deb9)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-1_exp6
in repository hdf5.

at  713deb9   (tag)
   tagging  6bf983c793865e753c39d49d5072bb0682d12448 (commit)
  replaces  debian/1.10.0-patch1+docs-1_exp5
 tagged by  Gilles Filippini
on  Sat Nov 26 21:01:49 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-1~exp6

Gilles Filippini (1):
  Fix FTBFS when building arch-all only

---

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[hdf5] annotated tag debian/1.10.0-patch1+docs-1_exp5 created (now 4b5492e)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-1_exp5
in repository hdf5.

at  4b5492e   (tag)
   tagging  df59eb7fa3ea84e0a5bd9f39b2302e808ac3e11d (commit)
  replaces  debian/1.10.0-patch1+docs-1_exp4
 tagged by  Gilles Filippini
on  Fri Nov 25 00:41:48 2016 +0100

- Log -
hdf5 Debian release 1.10.0-patch1+docs-1~exp5

Gilles Filippini (1):
  Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 CVE-2016-4333

---

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[hdf5] branch master-1.10 updated (9edc7e6 -> 6bf983c)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master-1.10
in repository hdf5.

  from  9edc7e6   Fix libhdf5-mpi-dev Depends field
   new  df59eb7   Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 
CVE-2016-4333
   new  6bf983c   Fix FTBFS when building arch-all only

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 debian/changelog |  14 +++
 debian/patches/CVE-2016-4330.patch   |  20 +++
 debian/patches/CVE-2016-4331-1.patch | 229 +++
 debian/patches/CVE-2016-4331-2.patch |  19 +++
 debian/patches/CVE-2016-4332.patch   |  37 ++
 debian/patches/CVE-2016-4333.patch   |  23 
 debian/patches/series|   5 +
 debian/rules |   3 +-
 8 files changed, 349 insertions(+), 1 deletion(-)
 create mode 100644 debian/patches/CVE-2016-4330.patch
 create mode 100644 debian/patches/CVE-2016-4331-1.patch
 create mode 100644 debian/patches/CVE-2016-4331-2.patch
 create mode 100644 debian/patches/CVE-2016-4332.patch
 create mode 100644 debian/patches/CVE-2016-4333.patch

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[hdf5] 02/02: Fix FTBFS when building arch-all only

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit 6bf983c793865e753c39d49d5072bb0682d12448
Author: Gilles Filippini <p...@debian.org>
Date:   Sat Nov 26 20:59:52 2016 +0100

Fix FTBFS when building arch-all only
---
 debian/changelog | 6 ++
 debian/rules | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index d413087..8c2d303 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+hdf5 (1.10.0-patch1+docs-1~exp6) experimental; urgency=medium
+
+  * Fix FTBFS when building arch-all only
+
+ -- Gilles Filippini <p...@debian.org>  Sat, 26 Nov 2016 20:58:15 +0100
+
 hdf5 (1.10.0-patch1+docs-1~exp5) experimental; urgency=medium
 
   * New patches CVE-2016-433*.patch from upstream develop branch
diff --git a/debian/rules b/debian/rules
index ed161bf..eea2244 100755
--- a/debian/rules
+++ b/debian/rules
@@ -239,7 +239,7 @@ define rename_h5p_helpers
  ) : 
 endef
 
-override_dh_install: $(foreach flavor,$(FLAVORS),dh_install_$(flavor))
+override_dh_install-arch: $(foreach flavor,$(FLAVORS),dh_install_$(flavor))
find debian/$(serpack)/usr/lib -name '*cpp*' -delete
 
 override_dh_makeshlibs:
@@ -266,6 +266,7 @@ install_doc:
 
 override_dh_auto_build-indep: build_doc
 override_dh_auto_install-indep: install_doc
+override_dh_install-indep: dh_install_serial
 
 
 override_dh_installchangelogs:

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[hdf5] 01/02: Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 CVE-2016-4333

[Gilles Filippini]

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pini pushed a commit to branch master-1.10
in repository hdf5.

commit df59eb7fa3ea84e0a5bd9f39b2302e808ac3e11d
Author: Gilles Filippini <p...@debian.org>
Date:   Fri Nov 25 00:37:12 2016 +0100

Fix CVE-2016-4330 CVE-2016-4331 CVE-2016-4332 CVE-2016-4333

New patches CVE-2016-433*.patch backported from related commits in
upstream develop branch.
---
 debian/changelog |   8 ++
 debian/patches/CVE-2016-4330.patch   |  20 +++
 debian/patches/CVE-2016-4331-1.patch | 229 +++
 debian/patches/CVE-2016-4331-2.patch |  19 +++
 debian/patches/CVE-2016-4332.patch   |  37 ++
 debian/patches/CVE-2016-4333.patch   |  23 
 debian/patches/series|   5 +
 7 files changed, 341 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index fda1951..d413087 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+hdf5 (1.10.0-patch1+docs-1~exp5) experimental; urgency=medium
+
+  * New patches CVE-2016-433*.patch from upstream develop branch
+to fix four vulnerabilities unveiled by TALOS (closes: #845301,
+CVE-2016-4330, CVE-2016-4331, CVE-2016-4332, CVE-2016-4333)
+
+ -- Gilles Filippini <p...@debian.org>  Thu, 24 Nov 2016 23:30:44 +0100
+
 hdf5 (1.10.0-patch1+docs-1~exp4) experimental; urgency=medium
 
   * Move setting of substvar ${hdf5-mpi-dev} into dh_makeshlib; it was
diff --git a/debian/patches/CVE-2016-4330.patch 
b/debian/patches/CVE-2016-4330.patch
new file mode 100644
index 000..cbc09b3
--- /dev/null
+++ b/debian/patches/CVE-2016-4330.patch
@@ -0,0 +1,20 @@
+commit b1eb1b3ee8693e2a56b074315b521c66255acca1
+Author: Neil Fortner <nfort...@hdfgroup.org>
+Date:   Thu Sep 1 17:24:24 2016 -0500
+
+Replace assertion in H5O_dtype_decode_helper for number of array 
dimensions with a check and error. The assertion was inappropriate because it 
is operating on data read from the file, which the library does not always have 
direct control of.
+
+diff --git a/src/H5Odtype.c b/src/H5Odtype.c
+index e51d319..eae542b 100644
+--- a/src/H5Odtype.c
 b/src/H5Odtype.c
+@@ -519,7 +519,8 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned 
*ioflags/*in,out*/, const uint8_t **p
+ dt->shared->u.array.ndims = *(*pp)++;
+ 
+ /* Double-check the number of dimensions */
+-HDassert(dt->shared->u.array.ndims <= H5S_MAX_RANK);
++if(dt->shared->u.array.ndims > H5S_MAX_RANK)
++HGOTO_ERROR(H5E_DATATYPE, H5E_CANTLOAD, FAIL, "too many 
dimensions for array datatype")
+ 
+ /* Skip reserved bytes, if version has them */
+ if(version < H5O_DTYPE_VERSION_3)
diff --git a/debian/patches/CVE-2016-4331-1.patch 
b/debian/patches/CVE-2016-4331-1.patch
new file mode 100644
index 000..078c982
--- /dev/null
+++ b/debian/patches/CVE-2016-4331-1.patch
@@ -0,0 +1,229 @@
+commit 2409f991667283f8fa1dacc66f245950693495aa
+Author: Neil Fortner <nfort...@hdfgroup.org>
+Date:   Thu Sep 8 10:48:54 2016 -0500
+
+Fix issues in H5Znbit.c where the decompression algorithm would not check 
the compressed data for validity, potentially causing a buffer overflow.
+
+Index: hdf5/src/H5Znbit.c
+===
+--- hdf5.orig/src/H5Znbit.c
 hdf5/src/H5Znbit.c
+@@ -60,11 +60,11 @@ static void H5Z_nbit_decompress_one_noop
+unsigned char *buffer, size_t *j, int *buf_len, 
unsigned size);
+ static void H5Z_nbit_decompress_one_atomic(unsigned char *data, size_t 
data_offset,
+ unsigned char *buffer, size_t *j, int *buf_len, 
parms_atomic p);
+-static void H5Z_nbit_decompress_one_array(unsigned char *data, size_t 
data_offset,
++static herr_t H5Z__nbit_decompress_one_array(unsigned char *data, size_t 
data_offset,
+unsigned char *buffer, size_t *j, int *buf_len, const unsigned 
parms[]);
+-static void H5Z_nbit_decompress_one_compound(unsigned char *data, size_t 
data_offset,
++static herr_t H5Z__nbit_decompress_one_compound(unsigned char *data, size_t 
data_offset,
+   unsigned char *buffer, size_t *j, int *buf_len, const unsigned 
parms[]);
+-static void H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, 
unsigned char *buffer,
++static herr_t H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, 
unsigned char *buffer,
+ const unsigned parms[]);
+ static void H5Z_nbit_compress_one_nooptype(unsigned char *data, size_t 
data_offset,
+  unsigned char *buffer, size_t *j, int *buf_len, unsigned 
size);
+@@ -990,7 +990,8 @@ H5Z_filter_nbit(unsigned flags, size_t c
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation 
failed for nbit decompression")
+ 
+ /* decompress the buffer */
+-

Bug#833457: hdf5: Please enable packaging of libhdf5-openmpi-dev on hppa arch

[Gilles Filippini]

Control: tags -1 confirmed

On Thu, 4 Aug 2016 17:33:58 +0200 Helge Deller  wrote:
> Package: hdf5
> Version: 1.8.16+docs-8
> Severity: normal
> 
> Can you please re-enable hppa as arch which builds libhdf5-openmpi-dev ?
> It breaks building other packages, and openmpi now builds on hppa (and m68k 
> and sh4).
> 
> The relevant lines in the debian/rules file are:
> ARCH_FLAG=-a
> # openmpi broken on archs hppa m68k sh4 (2016-02-24)
> OMPIARCHS?=any !hppa !m68k !sh4
> MPICHARCHS?=any

Will do after the upcoming hdf5-1.10 transition.

Thanks,

_g.



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[hdf5] annotated tag debian/1.10.0-patch1+docs-1_exp4 created (now 92780de)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-1_exp4
in repository hdf5.

at  92780de   (tag)
   tagging  9edc7e69b3b981e95a87502da6d05557a2832885 (commit)
  replaces  debian/1.10.0-patch1+docs-1_exp3
 tagged by  Gilles Filippini
on  Fri Jul 22 21:58:51 2016 +0200

- Log -
hdf5 Debian release 1.10.0-patch1+docs-1~exp4

Gilles Filippini (1):
  Fix libhdf5-mpi-dev Depends field

---

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[hdf5] 03/03: Upload release 1.10.0-patch1+docs-1~exp3 to experimental

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit 389a053da0b525f1fc51129bba2e0f225226b425
Author: Gilles Filippini <p...@debian.org>
Date:   Tue Jun 28 22:47:59 2016 +0200

Upload release 1.10.0-patch1+docs-1~exp3 to experimental
---
 debian/changelog | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 9763fd9..28ba166 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,11 @@
-hdf5 (1.10.0-patch1+docs-1~exp3) UNRELEASED; urgency=medium
+hdf5 (1.10.0-patch1+docs-1~exp3) experimental; urgency=medium
 
   * Set default plugins dir to /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/plugins
   * Symbols files:
 - CPP: use flag arch-its=64 instead of enumerating non 64 bits
   architectures
 
- -- Gilles Filippini <p...@debian.org>  Tue, 28 Jun 2016 21:02:05 +0200
+ -- Gilles Filippini <p...@debian.org>  Tue, 28 Jun 2016 22:47:41 +0200
 
 hdf5 (1.10.0-patch1+docs-1~exp2) experimental; urgency=medium
 

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Bug#826522: Set the plugin directory

[Gilles Filippini]

Jerome BENOIT a écrit le 29/06/2016 à 08:32 :
> Hi,
> 
> On 29/06/16 07:16, PICCA Frederic-Emmanuel wrote:
>>> I've juste uploaded release 1.10.0-patch1+docs-1~exp3 to experimental,
>>> configured with:
>>> --with-default-plugindir=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/plugins
> 
> 
>> Just for information do we have this plugin directory available in the 
>> pkg-config file in order to setup
>> the plugging directory for a third-party plugging project ?
> 
> 
> Should be easy to do, I guess.
> 
> Otherwise, would it be possible to add local plugins folder ?
> Something as:
> 
> --with-default-plugindir=/usr/local/lib/$(DEB_HOST_MULTIARCH)/hdf5/plugins:/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/plugins

No need to clutter it up. There is the environment variable HDF5_PLUGIN_PATH. 
From the HDF5 filters doc [1]:
> The default path can be overwritten by a user with the HDF5_PLUGIN_PATH 
> environment variable. Several directories can be specified for the search 
> path using “:” as a path separator for UNIX-like systems and “;” for Windows.

[1] 
https://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf

For now I'd rather stay with the above default configuration, until new real 
life cases are submitted.

Thanks,

_g.



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Bug#826522: Set the plugin directory

[Gilles Filippini]

Hi,

Jérôme Kieffer a écrit le 28/06/2016 à 09:16 :
> Dear HDF5 package maintainers,
> 
> Currently the debian build system does not enforce the plugin directory
> for HDF5 filters, defaulting to "/usr/local/hdf5/lib/plugin". I guess
> Debian would prefer something like:
> "/usr/share/hdf5/plugin" or even better:
> "/usr/lib/x86_64-linux-gnu/hdf5/plugins".
> 
> Would it be possible to specify the option 
> --with-default-plugindir=/usr/lib/x86_64-linux-gnu/hdf5/plugins
> to ./configure in order to re-locate those plugins and offer in
> external packages those plugins.
> 
> At synchrotrons, some of our detectors use LZ4 compression in HDF5
> files. Having plugins packaged and directly installable is real
> advantage compared to other operating systems.
> 
> Thanks for you comprehention.
> With my best regards,

I've juste uploaded release 1.10.0-patch1+docs-1~exp3 to experimental,
configured with:
--with-default-plugindir=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/plugins

Could you please give it a try?

Thanks,

_g.



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[hdf5] branch master-1.10 updated (3533146 -> 68c0d3a)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to branch master-1.10
in repository hdf5.

  from  3533146   Upload release 1.10.0-patch1+docs-1~exp1 to experimental
   new  b4eac7e   Symbols files: ignore -patch and ~(alpha|pre)
   new  1a7ad39   Update symbols files
   new  68c0d3a   Upload release 1.10.0-patch1+docs-1~exp2 to experimental

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/changelog   |   10 +
 debian/libhdf5-100.symbols | 3556 +--
 debian/libhdf5-cpp-100.symbols |  448 ++---
 debian/libhdf5-mpich-100.symbols   | 3626 ++--
 debian/libhdf5-openmpi-100.symbols | 3626 ++--
 debian/mangled-symbols-table   |  126 ++
 debian/map_serial.ver  |  126 ++
 debian/process-symbols-files   |2 +-
 debian/rules   |2 +-
 9 files changed, 5892 insertions(+), 5630 deletions(-)

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[hdf5] 03/03: Upload release 1.10.0-patch1+docs-1~exp2 to experimental

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit 68c0d3a33ee9a2bf408c05eb953b6a0edc92bd7a
Author: Gilles Filippini <p...@debian.org>
Date:   Tue May 24 23:59:35 2016 +0200

Upload release 1.10.0-patch1+docs-1~exp2 to experimental
---
 debian/changelog | 10 ++
 1 file changed, 10 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index cc0928c..3e1783b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+hdf5 (1.10.0-patch1+docs-1~exp2) experimental; urgency=medium
+
+  * Symbols files:
+- Drop ~alpha, ~pre and -patch parts of 1.10.0 release symbols.
+  They all belong to 1.10.0 release.
+- Reintroduce previously dropped cpp symbols, with flag
+  arch-bits!=64.
+
+ -- Gilles Filippini <p...@debian.org>  Tue, 24 May 2016 23:56:39 +0200
+
 hdf5 (1.10.0-patch1+docs-1~exp1) experimental; urgency=medium
 
   * New upstream release

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[hdf5] 01/03: Symbols files: ignore -patch and ~(alpha|pre)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a commit to branch master-1.10
in repository hdf5.

commit b4eac7ee3b936bb5f9bd5f65727b01dced552a71
Author: Gilles Filippini <p...@debian.org>
Date:   Tue May 24 23:41:15 2016 +0200

Symbols files: ignore -patch and ~(alpha|pre)
---
 debian/process-symbols-files | 2 +-
 debian/rules | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/process-symbols-files b/debian/process-symbols-files
index 3e990b8..dadbbd6 100755
--- a/debian/process-symbols-files
+++ b/debian/process-symbols-files
@@ -7,7 +7,7 @@ debian_dir="$(dirname "$(readlink -f "$0")")"
 cd "$debian_dir"
 
 # 2- Get version and sonames
-version="$(grep 'HDF5 config.lt' ../configure | awk '{print $3}' | sed -r 
's/-patch/./;s/-(alpha|pre)[0-9]*//')"
+version="$(grep 'HDF5 config.lt' ../configure | awk '{print $3}' | sed -r 
's/-patch[0-9]*//;s/-(alpha|pre)[0-9]*//')"
 soname=$(cd .. && ./debian/rules SONAME)
 soname_cxx=$(cd .. && ./debian/rules SONAME_CXX)
 
diff --git a/debian/rules b/debian/rules
index b4c6cc6..0fc472d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,7 +17,7 @@
 
 package = libhdf5
 pkgversion ?= $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-libversion ?= $(shell echo $(pkgversion) | sed 
's/^\([0-9\.]*\)\(~[^~+]*\)\?\(+docs[0-9]*\)\?-[^-]*$$/\1/')
+libversion ?= $(shell echo $(pkgversion) | sed -r 
's/^([0-9\.]*)([-~][^-~+]*)?(\+docs[0-9]*)?-[^-]*$$/\1/')
 
 # BEGIN - Get sonames from config/lt_vers.am
 include config/lt_vers.am

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[hdf5] annotated tag upstream/1.10.0-patch1+docs created (now 38613fe)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag upstream/1.10.0-patch1+docs
in repository hdf5.

at  38613fe   (tag)
   tagging  d2a3490c60e4b6ad3ed4e1881dab6f26987d5201 (commit)
  replaces  upstream/1.10.0+docs
 tagged by  Gilles Filippini
on  Sat May 21 15:28:38 2016 +0200

- Log -
Upstream version 1.10.0-patch1+docs

Gilles Filippini (1):
  Imported Upstream version 1.10.0-patch1+docs

---

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[hdf5] annotated tag debian/1.10.0-patch1+docs-1_exp1 created (now ff0eade)

[Gilles Filippini]

This is an automated email from the git hooks/post-receive script.

pini pushed a change to annotated tag debian/1.10.0-patch1+docs-1_exp1
in repository hdf5.

at  ff0eade   (tag)
   tagging  35331468a3101dd74d61ca358a2134ba25743010 (commit)
  replaces  debian/1.10.0+docs-1_exp3
 tagged by  Gilles Filippini
on  Sun May 22 10:48:31 2016 +0200

- Log -
hdf5 Debian release 1.10.0-patch1+docs-1~exp1

Gilles Filippini (14):
  Symbols files: fix archs alpha, kfreebsd-i386 and ppc64
  Symbols files: fix arch hppa
  Build-Depends-Indep: php-cli
  Symbols files: fix arch sparc64
  Symbols files: fix arch hurd-i386
  Symbols files: set same arch flags for openmpi and mpich
  Symbols files: fix arch m68k
  debian/changelog update
  Prepare import of upstream release 1.10.0-patch1
  Imported Upstream version 1.10.0-patch1+docs
  Merge tag 'upstream/1.10.0-patch1+docs' into master-1.10
  Update symbols files
  Standars-Version: 3.9.8
  Upload release 1.10.0-patch1+docs-1~exp1 to experimental

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