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Status of khmer


at the sprint Michael worked painstakingly on khmer packaging.  Since
all preconditions now arrived I had a look wearing my sponsoring hat.
Michael, please take a look at my commits killing all lintian issues.

Please gbp-pull and notice that I also created a *+dfsg tarball by
really removing third party zip libraries.

There are two remaining issues:

  1. DEP3 autopkgtest:
     I tried to add a test script in debian/test which should reproduce
     the call done in dh_auto_test.  Unfortunately it fails.  I assume
     this is easy to solve for you.

  2. The second issue is the seqan code copy.  Besides the fact that it
     would need to be mentioned in debian/copyright if it would remain
     I would really love to see if it could be removed as well as the
     zip library code copies.  From what I can see this is perfectly
     possible - at least the build (including the build-time test) works
     nicely with the following patch:

diff --git a/debian/control b/debian/control
index bacf509..bd9284b 100644
--- a/debian/control
+++ b/debian/control
@@ -16,7 +16,8 @@ Build-Depends: python-screed,
-               sphinxcontrib-autoprogram
+               sphinxcontrib-autoprogram,
+               seqan-dev
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/khmer.git
 Vcs-Git: git://anonscm.debian.org/debian-med/khmer.git
diff --git a/debian/patches/local-libs b/debian/patches/local-libs
index 31a0ce1..ffed4d3 100644
--- a/debian/patches/local-libs
+++ b/debian/patches/local-libs
@@ -1,9 +1,9 @@
 Description: Use Debian packaged libraries
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
---- khmer.orig/setup.cfg
-+++ khmer/setup.cfg
-@@ -7,10 +7,10 @@
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -7,10 +7,10 @@ attr = !known_failing,!jenkins
  undef = NO_UNIQUE_RC
@@ -13,7 +13,7 @@ Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 -include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include
 -# include-dirs = lib
 +#include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include
-+include-dirs = lib:third-party/seqan/core/include
++include-dirs = lib:/usr/include
  ## if using system libraries (broken)

Could you please make up your mind whether we could save the code copy
since we actually have the identical version number (I did not checked
the code!) packaged.

Kind regards



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