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Re: [Debian-med-packaging] Need help to update mhap package (build system changed from ant to maven)

On 07/12/2016 12:00 AM, Afif Elghraoui wrote:

> Just one more question: I'm also maintaining mhap in jessie-backports
> and it sounds like there will be trouble to build it on jessie if the
> maven artifacts are not present there. I can bring jaligner and
> libssw-java to jessie-backports. Does it make sense to backport
> libfastutil-java for this reason, or is there a workaround that can be
> done from within the mhap package for the backport?

Hello Afif,

For a work-around, you can often overcome the lack of maven artifacts by
explicitly telling maven how to resolve the dependency from the local
filesystem.  This is done by modifying the pom.xml to set <scope> to
"system" and <systemPath> appropriately for each build-dep JAR to find
in /usr/share/java.  An example is the patch attached.

Come to think of it, perhaps I should have suggested this initially.
However I think it's preferable to add the maven artifacts to the
dependencies when possible, since that prevents every reverse
build-dependency from having to create its own patch.  (That is, let the
build system do the work for you.)

In this case, it shouldn't be difficult to backport libfastutil-java if
you'd prefer that.

--- a/pom.xml
+++ b/pom.xml
@@ -110,6 +110,8 @@
+                        <scope>system</scope>
+                        <systemPath>/usr/share/java/fastutil.jar</systemPath>
@@ -125,13 +127,17 @@
+                        <scope>system</scope>
+                        <systemPath>/usr/share/java/jaligner.jar</systemPath>
+                        <scope>system</scope>
+                        <systemPath>/usr/share/java/ssw.jar</systemPath>
 	<description>MinHash alignment process (MHAP pronounced MAP): locality sensitive hashing to detect overlaps and utilities.</description>
\ No newline at end of file

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