[med-svn] [Git][med-team/seqan2][debian/jessie-backports] 116 commits: New upstream version 2.2.0+dfsg

Andreas Tille gitlab at salsa.debian.org
Mon Mar 26 11:46:23 UTC 2018 

Andreas Tille pushed to branch debian/jessie-backports at Debian Med / seqan2


Commits:
9a4a7481 by Andreas Tille at 2016-12-02T23:45:08+01:00
New upstream version 2.2.0+dfsg
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c804db8f by Michael R. Crusoe at 2017-01-14T03:43:56-08:00
New upstream version 2.3.0~0.20161011~73a5aaf+dfsg
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1d7cc220 by Michael R. Crusoe at 2017-01-14T03:43:56-08:00
New upstream version 2.3.0~0.20161019~af07bc1+dfsg
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d315dede by Michael R. Crusoe at 2017-01-14T03:43:56-08:00
New upstream version 2.3.1+dfsg
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c3694948 by Sascha Steinbiss at 2017-07-05T08:32:09+02:00
make build reproducible

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b70ac79b by Michael R. Crusoe at 2017-09-28T07:44:06-07:00
New upstream version 2.3.2+dfsg
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5db3cf73 by Michael R. Crusoe at 2017-09-28T07:46:18-07:00
Updated version 2.3.2+dfsg from 'upstream/2.3.2+dfsg'

with Debian dir 0811ffed9627e5c0994a1eff090e137026ff636c
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6d28a626 by Michael R. Crusoe at 2017-09-28T09:16:59-07:00
re-enable armel

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09c200d6 by Michael R. Crusoe at 2017-10-07T10:29:13-07:00
bye, armel; hello armhf

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e13c298f by Michael R. Crusoe at 2017-10-13T03:16:52-07:00
bye armhf; enforce & fix the tests

Fix tests to work with -DSEQAN_DISABLE_VERSION_CHECK=YES

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5f349621 by Michael R. Crusoe at 2017-10-13T04:38:14-07:00
New upstream version 2.3.2+dfsg2
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2a46319d by Michael R. Crusoe at 2017-10-13T04:40:17-07:00
Updated version 2.3.2+dfsg2 from 'upstream/2.3.2+dfsg2'

with Debian dir 9a75781a814c8c5ff88cfb9eb94aa8c96b8e0a41
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0a11a583 by Michael R. Crusoe at 2017-10-13T05:01:59-07:00
release

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0b62576d by Michael R. Crusoe at 2017-10-14T05:54:24-07:00
remove jinja2; async-io (sometimes)

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f945f143 by Michael R. Crusoe at 2017-10-23T09:27:28-07:00
New upstream version 2.3.2.000platform-issues0-8ae7bc0+dfsg1
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c7ad6053 by Michael R. Crusoe at 2017-10-23T09:35:31-07:00
Updated version 2.3.2.000platform-issues0-8ae7bc0+dfsg1 from 'upstream/2.3.2.000platform-issues0-8ae7bc0+dfsg1'

with Debian dir 4715d4eee1613a998c97a4407278a7a4e75e9047
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6c0a547a by Michael R. Crusoe at 2017-10-24T00:09:55-07:00
Test build of https://github.com/h-2/seqan/tree/fix/platform_issues

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50d0647d by Michael R. Crusoe at 2017-10-24T04:56:19-07:00
Backport debian/rules from experimental

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275e0e89 by Michael R. Crusoe at 2017-10-25T04:06:09-07:00
New upstream version 2.3.2.000platform-issues1-66a8baf+dfsg
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53ef67ba by Michael R. Crusoe at 2017-10-25T04:08:13-07:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues1-66a8baf+dfsg'

Update to upstream version '2.3.2.000platform-issues1-66a8baf+dfsg'
with Debian dir d0a5c0a4888237e7c609cd3d033d265f157adb28
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c8cb0dfc by Michael R. Crusoe at 2017-10-25T04:09:33-07:00
Additional fixes from upstream

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7a6c1f58 by Steffen Moeller at 2017-10-25T15:09:39+02:00
Added RRIDs

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be622bdc by Michael R. Crusoe at 2017-10-26T01:16:11-07:00
typo, -01 should have been -O1

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4a9ae400 by Michael R. Crusoe at 2017-10-26T01:22:19-07:00
disable razers on mips

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f129a454 by Michael R. Crusoe at 2017-10-26T03:06:38-07:00
temp allow parallel always

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23692a21 by Michael R. Crusoe at 2017-10-26T05:13:29-07:00
New upstream version 2.3.2.000platform-issues2-206d1f7+dfsg
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54089dd7 by Michael R. Crusoe at 2017-10-26T05:15:48-07:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues2-206d1f7+dfsg'

Update to upstream version '2.3.2.000platform-issues2-206d1f7+dfsg'
with Debian dir 35d80880c115a9b15d792fd4d5c7d6f4932344fa
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3ba33480 by Michael R. Crusoe at 2017-10-26T08:48:22-07:00
additional push from upstream

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eaae4ca1 by Michael R. Crusoe at 2017-10-26T23:41:02-07:00
re-enable parallel build override

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3cf71dc8 by Michael R. Crusoe at 2017-10-29T05:30:08-07:00
disable razer{,3} on mips; tweak arm{el,hf}

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ec19b5d1 by Michael R. Crusoe at 2017-11-02T10:42:25-07:00
document partial app skipping for mips

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b32d493f by Michael R. Crusoe at 2017-11-02T11:04:15-07:00
New upstream version 2.3.2.000platform-issues3-1d438c8+dfsg
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078a9fbe by Michael R. Crusoe at 2017-11-02T11:06:30-07:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues3-1d438c8+dfsg'

Update to upstream version '2.3.2.000platform-issues3-1d438c8+dfsg'
with Debian dir 740f0a1ff0d29a2148b8acb9c03646cbc19ba639
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1d691d69 by Michael R. Crusoe at 2017-11-02T11:41:31-07:00
new code from upstream

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a3a2a497 by Michael R. Crusoe at 2017-11-04T02:17:44-07:00
skip yara on armhf, sh4

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d555c954 by Michael R. Crusoe at 2017-11-05T08:22:13-08:00
Skip yara on armel

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b94ee537 by Michael R. Crusoe at 2017-11-06T11:52:53-08:00
New upstream version 2.3.2.000platform-issues4-fba8744+dfsg
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5eef82a7 by Michael R. Crusoe at 2017-11-06T11:55:19-08:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues4-fba8744+dfsg'

Update to upstream version '2.3.2.000platform-issues4-fba8744+dfsg'
with Debian dir f1b1ca31195adaef05c9c1e03c52f96f2a3601ae
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896e60b6 by Michael R. Crusoe at 2017-11-06T11:58:05-08:00
freshen upstream

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f0605098 by Michael R. Crusoe at 2017-11-06T12:15:51-08:00
Add test on sparc64 to aid debugging

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082378dd by Michael R. Crusoe at 2017-11-08T06:57:53-08:00
update sparc64 test, defines as per upstream

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e3580d12 by Michael R. Crusoe at 2017-11-08T06:58:20-08:00
New upstream version 2.3.2.000platform-issues5-86390dc+dfsg
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069f08d1 by Michael R. Crusoe at 2017-11-08T07:00:33-08:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues5-86390dc+dfsg'

Update to upstream version '2.3.2.000platform-issues5-86390dc+dfsg'
with Debian dir bd2caac6d65426dcd6b77c6448d168fe15f165ee
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9e19748c by Michael R. Crusoe at 2017-11-08T07:03:31-08:00
Another update from upstream

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49e1ab6f by Michael R. Crusoe at 2017-11-09T03:32:01-08:00
cleanup env vars

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8b125f4d by Michael R. Crusoe at 2017-11-10T00:49:48-08:00
Skip yara on kfreebsd-i386

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06d2ec67 by Michael R. Crusoe at 2017-11-10T01:00:06-08:00
Try out -O2 on archs that had been previously -O1

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b2ca48ca by Michael R. Crusoe at 2017-11-10T06:14:15-08:00
use seqan's built in manpage support

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723871cf by Michael R. Crusoe at 2017-11-11T05:39:58-08:00
fix typo

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c1d8a216 by Michael R. Crusoe at 2017-11-11T05:40:26-08:00
New upstream version 2.3.2.000platform-issues6-9cf5a69+dfsg
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072ceb6f by Michael R. Crusoe at 2017-11-11T05:42:40-08:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues6-9cf5a69+dfsg'

Update to upstream version '2.3.2.000platform-issues6-9cf5a69+dfsg'
with Debian dir 1267d9b88b993779fdc305a66f60a8663b3a51d2
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56831a02 by Michael R. Crusoe at 2017-11-11T05:44:40-08:00
>From upstream: another round of changes for the problems that affect all big endian.

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1bff7cfe by Michael R. Crusoe at 2017-11-18T04:50:59-08:00
-O3 for all, delete broken symlinks to fix manpage generation

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e3e3df8e by Michael R. Crusoe at 2017-11-18T06:19:50-08:00
type fix

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5b16e2c3 by Andreas Tille at 2017-11-20T09:14:37+01:00
This (not tested!) workaround does not answer the questions of the bug reporter but should cure the symptom

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4317cafc by Andreas Tille at 2017-11-20T09:15:25+01:00
d/rules: drop --parallel which is redundant for debhelper 10

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133a61b1 by Andreas Tille at 2017-11-21T21:54:33-08:00
This (not tested!) workaround does not answer the questions of the bug reporter but should cure the symptom

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40a4649d by Michael R. Crusoe at 2017-11-21T22:15:13-08:00
New upstream version 2.3.2.000platform-issues7-41f58c3+dfsg
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73751432 by Michael R. Crusoe at 2017-11-21T22:17:25-08:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues7-41f58c3+dfsg'

Update to upstream version '2.3.2.000platform-issues7-41f58c3+dfsg'
with Debian dir 8de8dc689b74872a88bde1d0af0cedab370bc938
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508f8848 by Michael R. Crusoe at 2017-11-21T22:19:37-08:00
one more time

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b3f954be by Andreas Tille at 2017-12-06T11:06:08+01:00
Fix indep-only build

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bd23584e by Andreas Tille at 2017-12-06T11:06:28+01:00
Upload to experimental

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ca43e4b1 by Andreas Tille at 2017-12-06T11:11:48+01:00
Do not generate manpages in arch indep builds (as done in experimental branch)

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5f328217 by Andreas Tille at 2017-12-06T11:12:24+01:00
Upload to unstable

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acb58c79 by Michael R. Crusoe at 2017-12-06T05:29:19-08:00
Merge remote-tracking branch 'origin/experimental' into experimental

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e738023b by Michael R. Crusoe at 2017-12-06T05:34:42-08:00
catch up with fixes from unstable

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9f5dc027 by Michael R. Crusoe at 2017-12-08T02:42:37-08:00
New upstream version 2.3.2.000platform-issues8-6f85721+dfsg
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6831e002 by Michael R. Crusoe at 2017-12-08T02:44:45-08:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues8-6f85721+dfsg'

Update to upstream version '2.3.2.000platform-issues8-6f85721+dfsg'
with Debian dir 4270d2cde5632a99bd07a2422da3d817f2293d87
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cbb003f8 by Michael R. Crusoe at 2017-12-08T04:41:23-08:00
Another update from upstream

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864446e3 by Michael R. Crusoe at 2017-12-14T01:51:39-08:00
force rebuild

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04b9d2f0 by Michael R. Crusoe at 2017-12-20T06:53:44-08:00
keep async, try a regular release

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817a28f1 by Michael R. Crusoe at 2017-12-20T07:25:55-08:00
New upstream version 2.3.2.000platform-issues9-028fd79+dfsg
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8e1ffee0 by Michael R. Crusoe at 2017-12-20T07:28:11-08:00
Update upstream source from tag 'upstream/2.3.2.000platform-issues9-028fd79+dfsg'

Update to upstream version '2.3.2.000platform-issues9-028fd79+dfsg'
with Debian dir c25558f6b078c9a290a77ec92bb85bbb8df1f95b
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efe35a2e by Michael R. Crusoe at 2017-12-20T07:40:33-08:00
another update from upstream

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30d3c43b by Michael R. Crusoe at 2017-12-20T23:59:50-08:00
switch to -DCMAKE_BUILD_TYPE=Release as per upstream

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b19650ac by Michael R. Crusoe at 2017-12-22T00:03:55-08:00
cleanup build flags

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49551449 by Michael R. Crusoe at 2018-01-03T09:11:34-08:00
New upstream version 2.3.2.001platform-issues10-6f85721+dfsg
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9b11d081 by Michael R. Crusoe at 2018-01-03T09:13:44-08:00
Update upstream source from tag 'upstream/2.3.2.001platform-issues10-6f85721+dfsg'

Update to upstream version '2.3.2.001platform-issues10-6f85721+dfsg'
with Debian dir 44be9185e1cf97bc5cc6e5e69231ab333c79c707
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37920383 by Michael R. Crusoe at 2018-01-03T09:27:37-08:00
hopefully final update from upstream before 2.4

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06b4aa44 by Michael R. Crusoe at 2018-01-04T05:11:49-08:00
enable asyncio everywhere & disable parallel building on powerpcspe

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194b7d53 by Michael R. Crusoe at 2018-01-26T09:42:46-08:00
New upstream version 2.4.0~rc0+dfsg
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dc253289 by Michael R. Crusoe at 2018-01-26T09:44:44-08:00
Update upstream source from tag 'upstream/2.4.0_rc0+dfsg'

Update to upstream version '2.4.0~rc0+dfsg'
with Debian dir 78da67cef37a7be02c018a184a43ff58be6f70b8
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6b7365e5 by Michael R. Crusoe at 2018-01-26T10:14:29-08:00
Testing upstream's formal release candidate

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63848311 by Michael R. Crusoe at 2018-01-30T02:57:24-08:00
New upstream version 2.4.0~rc1+dfsg
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109f05e7 by Michael R. Crusoe at 2018-01-30T02:59:17-08:00
Update upstream source from tag 'upstream/2.4.0_rc1+dfsg'

Update to upstream version '2.4.0~rc1+dfsg'
with Debian dir 89248c2d76ae2463a8d7a1c7f08bcbd856cc1db2
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90551756 by Michael R. Crusoe at 2018-01-30T03:00:57-08:00
Testing upstream's 2nd formal release candidate

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d20dbd5a by Michael R. Crusoe at 2018-01-31T04:18:42-08:00
Drop amd64, mips, mipsel to -j3 to save memory

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fcc93842 by Michael R. Crusoe at 2018-01-31T08:42:03-08:00
typo

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d7aab135 by Michael R. Crusoe at 2018-01-31T08:46:39-08:00
New upstream version 2.4.0~rc2+dfsg
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27a0a769 by Michael R. Crusoe at 2018-01-31T08:48:35-08:00
Update upstream source from tag 'upstream/2.4.0_rc2+dfsg'

Update to upstream version '2.4.0~rc2+dfsg'
with Debian dir 5fcff5f6e0e328629a8218a5328cc562436fb17a
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7e3cc84a by Michael R. Crusoe at 2018-01-31T22:37:58-08:00
Testing upstream's 3rd formal release candidate for 2.4.0

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26d12351 by Michael R. Crusoe at 2018-02-05T06:53:27-08:00
Merge branch 'experimental'

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1fe74e5e by Michael R. Crusoe at 2018-02-05T07:06:01-08:00
New upstream version 2.4.0+dfsg
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996ce03d by Michael R. Crusoe at 2018-02-05T07:08:05-08:00
Update upstream source from tag 'upstream/2.4.0+dfsg'

Update to upstream version '2.4.0+dfsg'
with Debian dir e9d0976e959e0576693ddaae86a348c42a1d8dc3
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22b00e1b by Michael R. Crusoe at 2018-02-05T07:52:29-08:00
2.4.0

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655bf275 by Michael R. Crusoe at 2018-02-05T11:53:14-08:00
fix pkgconfig

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a6fa2092 by Michael R. Crusoe at 2018-02-06T06:19:25-08:00
Install seqan-2.pc to /usr/share/pkgconfig as it is arch independent

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f197bc1e by Michael R. Crusoe at 2018-02-07T03:29:59-08:00
Drop mips{,el} down to 2 max parallel builds.

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fa67ffc2 by Michael R. Crusoe at 2018-02-08T03:57:02-08:00
mips{,el} max parallel⇒1, AMD64⇒2

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7e5f361c by Michael R. Crusoe at 2018-02-08T06:15:36-08:00
Update seqan-config.cmake installation location as per upstream

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490f784e by Michael R. Crusoe at 2018-02-09T03:54:01-08:00
Drop mips* to -O2 from -O3

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fdf585d4 by Michael R. Crusoe at 2018-02-10T10:38:00-08:00
Ship CWL descriptions for a subset of seqan-apps

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8940c0d5 by Michael R. Crusoe at 2018-02-10T10:50:13-08:00
skip mipsel due to lack of memory

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3ba52a4d by Michael R. Crusoe at 2018-02-11T02:56:53-08:00
skip mips due to lack of memory

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7a2518ab by Michael R. Crusoe at 2018-02-11T02:57:12-08:00
make executable example scripts

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0b161e58 by Michael R. Crusoe at 2018-02-16T04:27:47-08:00
Retry mips*; patch adapted from Adrian Bunk <bunk at debian.org>

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3441043b by Michael R. Crusoe at 2018-02-16T04:32:57-08:00
Document CWL generation. Mark all CWL files as executable

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777353ec by Michael R. Crusoe at 2018-02-16T05:08:12-08:00
add AutoPackageTests for seqan-apps

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a4b568f0 by Michael R. Crusoe at 2018-02-16T05:12:20-08:00
patch from upstream: add mandatory ctdVersion element.

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a6dab878 by Michael R. Crusoe at 2018-02-16T05:19:10-08:00
Suggest cwltool | cwl-runner

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faf937c1 by Michael R. Crusoe at 2018-02-16T05:35:43-08:00
Fix errors in manpage output

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553e776b by Michael R. Crusoe at 2018-02-17T07:10:14-08:00
release 2.4.0+dfsg-6

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7c5c8fa0 by Michael R. Crusoe at 2018-02-17T09:23:07-08:00
split arch/indep install

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8dee2cd3 by Michael R. Crusoe at 2018-02-19T02:15:23-08:00
Fix AutoPkgTests. Miscellaneous cleanups of debian/rules.

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0ef1b213 by Andreas Tille at 2018-03-26T11:37:54+02:00
Merge tag 'debian/2.4.0+dfsg-8' into debian/jessie-backports

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11237144 by Andreas Tille at 2018-03-26T11:38:48+02:00
Rebuild for jessie-backports

- - - - -


30 changed files:

- CHANGELOG.rst
- CMakeLists.txt
- LICENSE
- README.rst
- apps/alf/CMakeLists.txt
- apps/alf/LICENSE
- apps/alf/README
- apps/alf/alf.cpp
- apps/bs_tools/CMakeLists.txt
- apps/bs_tools/LICENSE
- apps/bs_tools/bisar.cpp
- apps/bs_tools/bisar.h
- apps/bs_tools/casbar.cpp
- apps/bs_tools/casbar.h
- apps/bs_tools/casbar_consensus_realign.h
- apps/bs_tools/casbar_score.h
- apps/bs_tools/four2three.cpp
- apps/dfi/CMakeLists.txt
- apps/dfi/README
- apps/fiona/CMakeLists.txt
- apps/fiona/compute_gain.cpp
- apps/fiona/fiona.cpp
- apps/fiona/index_qgram_parallel.h
- apps/fx_tools/CMakeLists.txt
- apps/fx_tools/LICENSE
- apps/fx_tools/fx_bam_coverage.cpp
- apps/fx_tools/fx_fastq_stats.cpp
- apps/gustaf/CMakeLists.txt
- apps/gustaf/LICENSE
- apps/gustaf/README


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/seqan2/compare/5edb530e7022c54cd5884499938daf70627c7bef...11237144a3e069bffa3f7dd65a817f9685639a7c

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View it on GitLab: https://salsa.debian.org/med-team/seqan2/compare/5edb530e7022c54cd5884499938daf70627c7bef...11237144a3e069bffa3f7dd65a817f9685639a7c
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