[Debian-med-packaging] Please consider tagging librdp-readseq releases

Andreas Tille andreas at an3as.eu
Wed Feb 25 08:26:24 UTC 2015

Hi Qiong,

thanks for your attempt to support our packaging effort.  I hope you do
not mind that I took the Debian Med development list into CC since there
are more people involved than me personally.

On Tue, Feb 24, 2015 at 04:13:11PM -0500, Qiong Wang wrote:
> The RDPTools is a module built upon a collection of repos. We expect our users to run git command to do updates. For example, to update to version 2.0.0, run these three commands to update the entire module:
> git checkout 2.0.0
> git submodule update --init
> make

Also for Debian packaging there is some workflow to create a package
right from a Git repository.  So in principle we could deliver packages
also that way.  However, this method is less established and has some
other side effects.

In any case in my mail from yesterday I wanted to make you aware that
something is wrong with the release you did tag yesterday at Github.
May be this is related to the nature of the project that it consists of
several separate repositories - but this is wild specualtion since I do
not have personal experience.  In any case I would recommend to fix the
download tarball - other users interested in the tarball might be fooled
by this empty download.  If you want I could throw this question to our
debian-mentors mailing list where several people with a lot of knowledge
about things like this are hanging around.
> If the Classifier is the primary repo that your group is interested,

Well, this might be a misunderstanding:  We are not a group with some
specific interest.  Debian Med tries to support any software which is
interesting in general in the field of biology and medicine.  So in
principle the whole suite of rdptools perfectly fits our scope and we
hope to do a service for you as developers of this software as well as
your users.

> and you setup only works with tar balls, we can tag the release for the Classifier and the three dependent package (AlignmentTools, ReadSeq and TaxonomyTree).  I have just tagged these packages as a start. 

Since Tim (in CC) just has prepared the packaging for ReadSeq I started
with this one just as a test.  We might reconsider our approach to
tackle the whole RDPTools suite if this might make more sense (which is
hard to decide for me alone).

Unfortunately when I tried to build ReadSeq I was stumbling upon a
problem when running the test suite (which is automatically done at
package build time):

ant -f junit-tmp.xml junit
Buildfile: /home/andreas/debian-maintain/repack/librdp-readseq-java/ReadSeq-2.0.0/junit-tmp.xml

    [javac] /home/andreas/debian-maintain/repack/librdp-readseq-java/ReadSeq-2.0.0/junit-tmp.xml:7: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 15 source files
    [javac] Note: /home/andreas/debian-maintain/repack/librdp-readseq-java/ReadSeq-2.0.0/test/edu/msu/cme/rdp/readseq/utils/gbregion/JoinRegionTest.java uses unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [junit] Running edu.msu.cme.rdp.readseq.IndexedSeqReaderTest
    [junit] Indexed 5 sequences in 1 ms
    [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,122 sec
    [junit] Running edu.msu.cme.rdp.readseq.SequenceParserTest
    [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,075 sec
    [junit] Running edu.msu.cme.rdp.readseq.readers.QSeqReaderTest
    [junit] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0,068 sec

/home/andreas/debian-maintain/repack/librdp-readseq-java/ReadSeq-2.0.0/junit-tmp.xml:11: Test edu.msu.cme.rdp.readseq.readers.QSeqReaderTest failed

Do you have any idea what might went wrong here?

Kind regards and thanks for your support


> On Feb 24, 2015, at 3:37 PM, Andreas Tille <andreas at an3as.eu> wrote:
> > Hi Qiong,
> > 
> > thanks for your intend to help.
> > 
> > On Tue, Feb 24, 2015 at 11:29:22AM -0500, Qiong Wang wrote:
> >> Thank you for your inquiry about tagging our releases on GitHub. Since many RDP tools are dependent on other tools from RDP, we created a tool module called RDPTools to make it easy for our users to install and update on their local system. We plan to only tag releases in RDPTools repo. We will follow the major.minor.patch versioning recommended by Git. Please take a look at the current tag 2.0.0 from https://github.com/rdpstaff/RDPTools/releases. Let us know if that works for you. 
> > 
> > In principle it would be OK to collect different modules in one main
> > release tarball.  However, somehow seems to be broken with the creation
> > of this tarball since the download has only 1710 Bytes and all subdirs
> > are empty.
> > 
> > BTW, our actual target is rdpclassifier anyway since it is used by
> > Qiime which we are packaging as well.
> > 
> > Kind regards
> > 
> >     Andreas.
> > 
> > -- 
> > http://fam-tille.de


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