[med-svn] [seqan] branch master updated (3caf497 -> a234c30)

Andreas Tille tille at debian.org
Wed Jul 27 09:19:17 UTC 2016


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

tille pushed a change to branch master
in repository seqan.

      from  3caf497   d/rules: Add -DNDEBUG to cflags and enable parallel build
       new  b073b60   Build needs header file from stellar core app - so leave this inside source package
       new  7461269   Imported Upstream version 1.4.2+dfsg
       new  84a59c5   Merge tag 'upstream/1.4.2+dfsg'
       new  fb2e30e   Remove outdated comments
       new  2e65f24   The old seqan version should only provide development tools, no doc needed
       new  b9d9d92   Moved debian/upstream to debian/upstream/metadata
       new  630a793   Update changelog
       new  923d6b3   Imported Upstream version 1.4.2+dfsg
       new  17d1fcb   Merge tag 'upstream/1.4.2+dfsg'
       new  5167612   Do not try to make docs
       new  c38d134   seqan-apps binary package is not shipped any more
       new  854fbbc   Remove some removed files from d/copyright, remove more unused files from source that just creat extra work in adding copyright notices
       new  5590ca3   Imported Upstream version 1.4.2+dfsg
       new  5b15f44   Merge tag 'upstream/1.4.2+dfsg'
       new  9adaf06   Overhaul of copyright
       new  a234c30   DEP3

The 16 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:
 core/apps/stellar/stellar.cpp                      |    729 +
 core/apps/stellar/stellar.h                        |    760 +
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 delete mode 100644 util/py_lib/seqan/dox/tpl/lib/jquery-bbq/unit/jquery-1.4.1.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/lib/jquery-bbq/unit/qunit.css
 delete mode 100644 util/py_lib/seqan/dox/tpl/lib/jquery-bbq/unit/unit.js
 delete mode 100755 util/py_lib/seqan/dox/tpl/lib/styles.less
 delete mode 100644 util/py_lib/seqan/dox/tpl/list.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/macro.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/metafunction.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/page.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/sections.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/shortcut.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/sub_entries.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/tag.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/typedef.html
 delete mode 100644 util/py_lib/seqan/dox/tpl/variable.html
 delete mode 100644 util/py_lib/seqan/dox/write_html.py

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