[med-svn] [Git][med-team/community/helper-scripts][master] automatic update

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
a5fc38f0 by Andreas Tille at 2024-07-06T01:43:17+00:00
automatic update

- - - - -


4 changed files:

- debian-med-tests.txt
- debian-science-tests.txt
- outdated_med-packages.txt
- python-team-tests.txt


Changes:

=
debian-med-tests.txt
=
@@ -1,4 +1,4 @@
-Last-Update: Fri, 05 Jul 2024 13:42:05 +
+Last-Update: Sat, 06 Jul 2024 01:42:04 +
 
  Source| Vote   | Tasks
  | Tags 
 
---+++--


=
debian-science-tests.txt
=
@@ -1,4 +1,4 @@
-Last-Update: Fri, 05 Jul 2024 13:42:10 +
+Last-Update: Sat, 06 Jul 2024 01:42:04 +
 
Source  | Vote   | Tasks
   |  Tags  
 
 
---++-+-


=
outdated_med-packages.txt
=
The diff for this file was not included because it is too large.

=
python-team-tests.txt
=
@@ -1,4 +1,4 @@
-Last-Update: Fri, 05 Jul 2024 13:42:13 +
+Last-Update: Sat, 06 Jul 2024 01:42:05 +
 
  Source | Vote   |  
Tags  
 
++



View it on GitLab: 
https://salsa.debian.org/med-team/community/helper-scripts/-/commit/a5fc38f0f11a1a31eab3d05746dfb800aa0c597f

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[med-svn] [Git][med-team/orthanc-wsi] Pushed new tag debian/2.0+dfsg-3

[Sebastien Jodogne (@jodogne-guest)]

Sebastien Jodogne pushed new tag debian/2.0+dfsg-3 at Debian Med / orthanc-wsi

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[med-svn] [Git][med-team/orthanc-wsi][master] 2 commits: added dependency on libpng-dev and libssl-dev

[Sebastien Jodogne (@jodogne-guest)]

Sebastien Jodogne pushed to branch master at Debian Med / orthanc-wsi


Commits:
3f08ed77 by jodogne-guest at 2024-07-06T00:51:06+02:00
added dependency on libpng-dev and libssl-dev

- - - - -
9a51e387 by jodogne-guest at 2024-07-06T00:56:28+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/control
- + debian/source/include-binaries


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+orthanc-wsi (2.0+dfsg-3) unstable; urgency=medium
+
+  * Added dependency on libpng-dev and libssl-dev. Closes: #1075794
+
+ -- Sebastien Jodogne   Sat, 06 Jul 2024 00:49:54 +0200
+
 orthanc-wsi (2.0+dfsg-2) unstable; urgency=medium
 
   * Team upload.


=
debian/control
=
@@ -10,6 +10,8 @@ Build-Depends: cmake,
libdcmtk-dev,
libopenjp2-7-dev,
liborthancframework-dev (>= 1.9.4),
+   libpng-dev,
+   libssl-dev,
libtiff-dev,
orthanc-dev,
uuid-dev,


=
debian/source/include-binaries
=
@@ -0,0 +1 @@
+debian-tests-data/CMU-1-Small-Region.tiff



View it on GitLab: 
https://salsa.debian.org/med-team/orthanc-wsi/-/compare/f09461a8b37846671b3afb031f403dcb5af44230...9a51e387c85cc6070b9f28cd6d981175cfdd116e

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[med-svn] [Git][med-team/orthanc][master] 2 commits: added dependency on libssl-dev

[Sebastien Jodogne (@jodogne-guest)]

Sebastien Jodogne pushed to branch master at Debian Med / orthanc


Commits:
b56a4fdd by jodogne-guest at 2024-07-05T23:58:57+02:00
added dependency on libssl-dev

- - - - -
8df9e543 by jodogne-guest at 2024-07-06T00:13:29+02:00
Upload to unstable

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
@@ -1,3 +1,9 @@
+orthanc (1.12.4+dfsg-2) unstable; urgency=medium
+
+  * Added dependency on libssl-dev. Closes: #1075795
+
+ -- Sebastien Jodogne   Fri, 05 Jul 2024 23:57:08 +0200
+
 orthanc (1.12.4+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=
debian/control
=
@@ -21,6 +21,7 @@ Build-Depends: cmake,
libprotobuf-dev,
libpugixml-dev,
libsqlite3-dev,
+   libssl-dev,
libwrap0-dev,
locales,
protobuf-compiler,



View it on GitLab: 
https://salsa.debian.org/med-team/orthanc/-/compare/9efc2576d1027675c852d8d5e6d7ae4ee85e21fc...8df9e543b2fa2ea5a68cf1c4023e3090f357d037

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[med-svn] [Git][med-team/orthanc] Pushed new tag debian/1.12.4+dfsg-2

[Sebastien Jodogne (@jodogne-guest)]

Sebastien Jodogne pushed new tag debian/1.12.4+dfsg-2 at Debian Med / orthanc

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[med-svn] [Git][med-team/dialign][master] 2 commits: hardening.patch: update to include CPPFLAGS.

[@emollier]

Étienne Mollier pushed to branch master at Debian Med / dialign


Commits:
b61b3f0a by Étienne Mollier at 2024-07-05T19:26:07+02:00
hardening.patch: update to include CPPFLAGS.

This allows fortifying functions.

- - - - -
31fc73a7 by Étienne Mollier at 2024-07-05T19:28:00+02:00
update changelog

- - - - -


2 changed files:

- debian/changelog
- debian/patches/hardening.patch


Changes:

=
debian/changelog
=
@@ -1,3 +1,10 @@
+dialign (2.2.1-14) UNRELEASED; urgency=medium
+
+  * hardening.patch: update to include CPPFLAGS.
+This allows fortifying functions.
+
+ -- Étienne Mollier   Fri, 05 Jul 2024 19:26:37 +0200
+
 dialign (2.2.1-13) unstable; urgency=medium
 
   * d/control: declare compliance to standards version 4.7.0.


=
debian/patches/hardening.patch
=
@@ -1,9 +1,11 @@
-Author: Andreas Tille 
-LastChanged: Thu, 14 Nov 2013 13:23:16 +0100
 Description: Propagate hardening options
+Author: Andreas Tille 
+Forwarded: no
+Reviewed-By: Étienne Mollier 
+Last-Update: 2024-07-05
 
 a/src/makefile
-+++ b/src/makefile
+--- dialign.orig/src/makefile
 dialign/src/makefile
 @@ -11,7 +11,7 @@
  
  
@@ -13,7 +15,7 @@ Description: Propagate hardening options
  #CFLAGS =  -g -c -I$ -DCONS
  LIBS = -lm
  #
-@@ -23,7 +23,7 @@ OBJS = dialign.o functions.o  para.o \
+@@ -23,7 +23,7 @@
  
  #
  dialign2-2: $(OBJS)  
@@ -22,3 +24,36 @@ Description: Propagate hardening options
  # $(CC) -g $(OBJS) $(LIBS) -o dialign2-2_db
  #
  #
+@@ -31,23 +31,23 @@
+ #
+ 
+ dialign.o: dialign.c
+-  $(CC) $(CFLAGS) dialign.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) dialign.c
+ functions.o: functions.c 
+-  $(CC) $(CFLAGS) functions.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) functions.c
+ input.o: input.c
+-  $(CC) $(CFLAGS) input.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) input.c
+ frag_chain.o: frag_chain.c
+-  $(CC) $(CFLAGS) frag_chain.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) frag_chain.c
+ para.o: para.c
+-  $(CC) $(CFLAGS) para.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) para.c
+ output.o: output.c
+-  $(CC) $(CFLAGS) output.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) output.c
+ wgt.o: wgt.c
+-  $(CC) $(CFLAGS) wgt.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) wgt.c
+ regex.o: regex.c
+-  $(CC) $(CFLAGS) regex.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) regex.c
+ anchor.o: anchor.c
+-  $(CC) $(CFLAGS) anchor.c
++  $(CC) $(CPPFLAGS) $(CFLAGS) anchor.c
+ 
+ #
+ 



View it on GitLab: 
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[med-svn] [Git][med-team/python-cogent] Pushed new tag debian/2024.5.7a1+dfsg-3

[Santiago Vila (@sanvila)]

Santiago Vila pushed new tag debian/2024.5.7a1+dfsg-3 at Debian Med / 
python-cogent

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[med-svn] [Git][med-team/python-cogent][master] 2 commits: Update skip-parallel-tests-on-single-cpu-systems.patch to skip...

[Santiago Vila (@sanvila)]

Santiago Vila pushed to branch master at Debian Med / python-cogent


Commits:
8da22a9e by Santiago Vila at 2024-07-05T18:48:15+02:00
Update skip-parallel-tests-on-single-cpu-systems.patch to skip 
"test_write_db_parallel" again. Closes: #1030885.

- - - - -
61224724 by Santiago Vila at 2024-07-05T18:49:27+02:00
Upload to unstable as 2024.5.7a1+dfsg-3

- - - - -


2 changed files:

- debian/changelog
- debian/patches/skip-parallel-tests-on-single-cpu-systems.patch


Changes:

=
debian/changelog
=
@@ -1,3 +1,11 @@
+python-cogent (2024.5.7a1+dfsg-3) unstable; urgency=medium
+
+  * Team upload.
+  * Update skip-parallel-tests-on-single-cpu-systems.patch
+to skip "test_write_db_parallel" again. Closes: #1030885.
+
+ -- Santiago Vila   Fri, 05 Jul 2024 18:45:00 +0200
+
 python-cogent (2024.5.7a1+dfsg-2) unstable; urgency=medium
 
   * Fix binary-any build


=
debian/patches/skip-parallel-tests-on-single-cpu-systems.patch
=
@@ -1,11 +1,55 @@
 Author: Santiago Vila 
-Last-Update: 2023-10-28
+Last-Update: 2024-07-05
 Bug-Debian: https://bugs.debian.org/1030885
 Description: Skip parallel tests on single-cpu systems
 
+--- a/tests/test_app/test_evo.py
 b/tests/test_app/test_evo.py
+@@ -2,10 +2,11 @@
+ 
+ from os.path import dirname, join
+ from tempfile import TemporaryDirectory
+-from unittest import TestCase
++from unittest import TestCase, skipIf
+ from unittest.mock import MagicMock
+ 
+ import pytest
++import multiprocessing
+ 
+ from numpy.testing import assert_allclose, assert_raises
+ 
+@@ -846,6 +847,7 @@
+ _ = io.load_db() + evo_app.bootstrap(hyp, num_reps=2) + writer
+ 
+ 
++@skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu 
systems")
+ def test_bstrap_parallel():
+ """exercising bootstrap with parallel"""
+ aln = load_aligned_seqs(join(data_dir, "brca1.fasta"), moltype="dna")
+--- a/tests/test_app/test_io.py
 b/tests/test_app/test_io.py
+@@ -9,8 +9,10 @@
+ 
+ import numpy
+ import pytest
++import multiprocessing
+ 
+ from numpy.testing import assert_allclose
++from unittest import skipIf
+ 
+ from cogent3 import DNA, get_app, open_data_store
+ from cogent3.app import io as io_app
+@@ -481,6 +483,7 @@
+ assert isinstance(writer.data_store.summary_not_completed, Table)
+ 
+ 
++@skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu 
systems")
+ def test_write_db_parallel(tmp_dir, fasta_dir):
+ """writing with overwrite in parallel should reset db"""
+ dstore = open_data_store(fasta_dir, suffix="fasta")
 --- a/tests/test_util/test_parallel.py
 +++ b/tests/test_util/test_parallel.py
-@@ -25,6 +25,7 @@ def check_is_master_process(n):
+@@ -25,6 +25,7 @@
  
  
  class ParallelTests(TestCase):
@@ -13,7 +57,7 @@ Description: Skip parallel tests on single-cpu systems
  def test_create_processes(self):
  """Procressor pool should create multiple distingue processes"""
  max_worker_count = multiprocessing.cpu_count() - 1
-@@ -35,6 +36,7 @@ class ParallelTests(TestCase):
+@@ -35,6 +36,7 @@
  self.assertEqual(sorted(list(result_values)), index)
  self.assertEqual(len(set(result_processes)), max_worker_count)
  
@@ -21,7 +65,7 @@ Description: Skip parallel tests on single-cpu systems
  def test_random_seeding(self):
  """Random seed should be set every function call"""
  # On Windows process ids are not guaranteed to be 
sequential(1,2,3,4...)
-@@ -46,6 +48,7 @@ class ParallelTests(TestCase):
+@@ -46,6 +48,7 @@
  self.assertEqual(result1[0], result2[0])
  self.assertNotEqual(result1, result2)
  
@@ -29,26 +73,3 @@ Description: Skip parallel tests on single-cpu systems
  @skipIf(sys.version_info[1] < 7, "method exclusive to Python 3.7 and 
above")
  def test_is_master_process(self):
  """
 a/tests/test_app/test_evo.py
-+++ b/tests/test_app/test_evo.py
-@@ -2,10 +2,11 @@ import pathlib
- 
- from os.path import dirname, join
- from tempfile import TemporaryDirectory
--from unittest import TestCase
-+from unittest import TestCase, skipIf
- from unittest.mock import MagicMock
- 
- import pytest
-+import multiprocessing
- 
- from numpy.testing import assert_allclose, assert_raises
- 
-@@ -846,6 +847,7 @@ class TestBootstrap(TestCase):
- _ = io.load_db() + evo_app.bootstrap(hyp, num_reps=2) + writer
- 
- 
-+@skipIf(multiprocessing.cpu_count() == 1, "Does not work on single-cpu 
systems")
- def test_bstrap_parallel():
- """exercising bootstrap with parallel"""
- aln = load_aligned_seqs(join(data_dir, "brca1.fasta"), moltype="dna")



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[med-svn] [Git][med-team/libbpp-phyl-omics] Pushed new tag debian/2.4.1-7

[Andreas Tille (@tille)]

Andreas Tille pushed new tag debian/2.4.1-7 at Debian Med / libbpp-phyl-omics

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[med-svn] [Git][med-team/pycorrfit][master] remove non-standard-dir-in-usr and move PyCorrFit_doc.pdf to share/doc

[vimerbf (@vimerbf-guest)]

vimerbf pushed to branch master at Debian Med / pycorrfit


Commits:
0542ecde by Bo YU at 2024-07-05T19:41:08+08:00
remove non-standard-dir-in-usr and move PyCorrFit_doc.pdf to share/doc

Signed-off-by: Bo YU 

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=
debian/changelog
=
@@ -1,11 +1,13 @@
 pycorrfit (1.1.7+dfsg-3) unstable; urgency=medium
 
   * Team upload.
-  
+
   [ Bo YU]
-  * Add python3-zombie-imp to workaround to fix ftbfs. 
+  * Add python3-zombie-imp to workaround to fix ftbfs.
(Closes: #1074222). Thanks Andreas Tille and Alexandre Detiste.
-   
+  * Remove usr/pycorrfit_doc/ dir and copy PyCorrFit_doc.pdf to
+/share/doc
+
   [ Andreas Tille ]
   * Standards-Version: 4.7.0 (routine-update)
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)


=
debian/rules
=
@@ -63,6 +63,11 @@ override_dh_install:
debian/$(DEB_SOURCE)/usr/share/pixmaps
rm -vf 
$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/pycorrfit/readfiles/read_pt3_scripts/README
 
+execute_after_dh_install:
+   mv $(CURDIR)/debian/$(DEB_SOURCE)/usr/pycorrfit_doc/PyCorrFit_doc.pdf \
+  $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/pycorrfit
+   rm -rf $(CURDIR)/debian/$(DEB_SOURCE)/usr/pycorrfit_doc
+
 override_dh_fixperms:
dh_fixperms
find debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples -type f 
-name "*.txt" -exec chmod 644 \{\} \;



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[med-svn] [Git][med-team/dcmtk][master] 46 commits: d/watch: Point to git HEAD

[Mathieu Malaterre (@malat)]

Mathieu Malaterre pushed to branch master at Debian Med / dcmtk


Commits:
4e1a995b by Mathieu Malaterre at 2022-10-18T11:41:28+02:00
d/watch: Point to git HEAD

- - - - -
a4a0cc0d by Mathieu Malaterre at 2022-10-18T11:41:47+02:00
Update upstream source from tag 'upstream/3.6.8_git20221013.51be018'

Update to upstream version '3.6.8~git20221013.51be018'
with Debian dir c1456c6cff83acea3f9836a016d4bf58de9077be
- - - - -
1e445425 by Mathieu Malaterre at 2022-10-18T11:41:47+02:00
New upstream version 3.6.8~git20221013.51be018
- - - - -
727ff077 by Mathieu Malaterre at 2022-11-07T10:47:45+01:00
d/rules: Add dcmtk-data package

- - - - -
49fcfd87 by Mathieu Malaterre at 2022-11-07T10:50:28+01:00
d/install: Start migrating to new 18 ABI

- - - - -
c608bcb8 by Mathieu Malaterre at 2022-11-07T10:51:32+01:00
d/patches: Add fake version mechanism

- - - - -
0ae3fe54 by Mathieu Malaterre at 2022-11-07T10:53:30+01:00
d/changelog: Upload 3.6.8~git20221013.51be018-1 to experimental

- - - - -
5123953f by Mathieu Malaterre at 2022-11-07T11:26:14+01:00
d/lintian: Make sure to override lintian/ijg check

- - - - -
bdf52283 by Mathieu Malaterre at 2022-11-07T11:28:03+01:00
d/control: Add missing dependency on libjs-jquery. Closes: #989108

- - - - -
5b090a05 by Mathieu Malaterre at 2022-11-07T13:32:41+01:00
d/changelog: Upload 3.6.8~git20221013.51be018-2 to experimental

- - - - -
8240cdce by Mathieu Malaterre at 2022-11-07T13:33:25+01:00
d/doc-base: Fix full path

- - - - -
473ab1fe by Mathieu Malaterre at 2022-11-07T13:33:52+01:00
d/changelog: Upload 3.6.8~git20221013.51be018-3 to experimental

- - - - -
eb7fc286 by Mathieu Malaterre at 2022-11-07T16:38:33+01:00
Update upstream source from tag 'upstream/3.6.8_git20221024.b8950f9'

Update to upstream version '3.6.8~git20221024.b8950f9'
with Debian dir 9a64612beb1cdfcc4385edb6601fc50340ae3c8e
- - - - -
4d10e36c by Mathieu Malaterre at 2022-11-07T16:38:33+01:00
New upstream version 3.6.8~git20221024.b8950f9
- - - - -
de0b624c by Mathieu Malaterre at 2022-11-07T16:38:53+01:00
d/patches: Refresh version for new snapshot

- - - - -
eedbde61 by Mathieu Malaterre at 2022-11-07T16:39:15+01:00
d/changelog: Upload 3.6.8~git20221024.b8950f9-1 to experimental

- - - - -
f0327354 by Mathieu Malaterre at 2023-06-30T09:41:53+00:00
d/control: Reduce number of dependencies for -dev package

- - - - -
ab2fd2a6 by Mathieu Malaterre at 2023-06-30T14:05:27+02:00
d/rules: Remove gnu extensions, only strict c++17

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60605fae by Mathieu Malaterre at 2023-06-30T12:18:42+00:00
d/rules: Do not build test suite if not required

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f22531de by Mathieu Malaterre at 2023-06-30T14:19:18+02:00
d/changelog: Upload 3.6.8~git20221024.b8950f9-2 to experimental

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a6c884e2 by Mathieu Malaterre at 2023-06-30T15:26:50+02:00
d/patches: Remove obsolete/unused patches

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21a0e3b9 by Mathieu Malaterre at 2023-06-30T15:27:06+02:00
d/rules: Fix debuild -A (all)

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e6af2e43 by Mathieu Malaterre at 2023-06-30T15:27:41+02:00
d/changelog: Upload 3.6.8~git20221024.b8950f9-3 to experimental

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b516ac9b by Mathieu Malaterre at 2023-11-06T09:21:23+01:00
Update upstream source from tag 'upstream/3.6.8_git20231027.1549d8c'

Update to upstream version '3.6.8~git20231027.1549d8c'
with Debian dir fc782cdbeb7763e3df9730ee289589274a82634b
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53c26ca1 by Mathieu Malaterre at 2023-11-06T09:21:23+01:00
New upstream version 3.6.8~git20231027.1549d8c
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f0f9dfaa by Mathieu Malaterre at 2023-11-06T10:25:50+01:00
d/patches: Remove version from install paths

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079527fb by Mathieu Malaterre at 2023-11-06T10:27:28+01:00
d/rules: Start using LTO

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65eb9aab by Mathieu Malaterre at 2023-11-06T10:28:25+01:00
d/changelog: Upload 3.6.8~git20231027.1549d8c-1 to experimental

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2318cc44 by Mathieu Malaterre at 2023-11-06T12:04:04+01:00
d/patches: Fix install path for docs

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0ea5fd8d by Mathieu Malaterre at 2023-11-06T12:07:55+01:00
d/changelog: Upload 3.6.8~git20231027.1549d8c-2 to experimental

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2ffc893b by Mathieu Malaterre at 2024-01-11T15:40:43+01:00
New upstream version 3.6.8
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67a6f7c4 by Mathieu Malaterre at 2024-01-11T15:40:43+01:00
Update upstream source from tag 'upstream/3.6.8'

Update to upstream version '3.6.8'
with Debian dir 9197f93b8f3af0afd6f1f4f0edb87e66c45db77f
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33a56d33 by Mathieu Malaterre at 2024-01-11T15:41:58+01:00
d/patches: Refresh patches

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b5de3ce3 by Mathieu Malaterre at 2024-01-11T16:08:30+01:00
d/changelog: Upload 3.6.8-1 to experimental

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55e72fc5 by Mathieu Malaterre at 2024-01-12T10:33:11+01:00
d/rules: Fix test suite on x87 hardware

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2dce6668 by Mathieu Malaterre at 2024-01-12T10:33:52+01:00
d/patches: Import bug fix from upstream

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0616f774 by Mathieu Malaterre at 2024-01-12T10:34:53+01:00
d/changelog: Upload 3.6.8-2 to experimental

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42583dfe by Emanuele Rocca at 2024-01-12T17:08:37+01:00
d/rules: Fix armel buildd

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f4c27faa by Mathieu Ma

[med-svn] [Git][med-team/dcmtk] Pushed new tag debian/3.6.8-5

[Mathieu Malaterre (@malat)]

Mathieu Malaterre pushed new tag debian/3.6.8-5 at Debian Med / dcmtk

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