Re: questions regarding packaging

["Dr. med. Christoph Gille" <christoph.gille@charite.de>]

Thanks Andreas,

>As an additional note I wonder whether it is a really good idea from a
>QA point of view to relay your strap software on unmaintained alpha code.

Neobio is used in Strap to make alignments of two sequences.  Since it
is a java library, it avoids the overhead of starting a huge program
like clustalw.  I would not mind using any other library, but I have
not spotted an appropriate library for aligning sequences which is (1)
in java (2) runs fast and (3) is already packaged in debian. If
someone knows an existing debian package, I could use it in Strap.



>The downloading is a separate step:
>    make -f debian/rules get-orig-source
>However (2) and (3) are in most cases on step which is triggered instance by
>    debuild


I tested these two commands on some packages like bowtie but it did
not work:

c@n:~/testSvn2/trunk/packages/bowtie/trunk$ debuild
   This package has a Debian revision number but there does not seem to be
   an appropriate original tar file or .orig directory in the parent directory;
   (expected one of bowtie_0.12.7.orig.tar.gz, ...

I copy the file from tarballs and try again
c@n:~/testSvn2/trunk/packages/bowtie/trunk$ ln
../tarballs/bowtie_0.12.7.orig.tar.gz ..

c@n:~/testSvn2/trunk/packages/bowtie/trunk$ debuild

       dh build
          dh_testdir
          dh_auto_configure
          debian/rules override_dh_auto_build
       make[1]: Entering directory `/home/c/testSvn2/trunk/packages/bowtie/trunk'
       /usr/bin/make allall
       make[2]: Entering directory `/home/c/testSvn2/trunk/packages/bowtie/trunk'
       make[2]: *** No rule to make target `allall'.  Stop.
       make[2]: Leaving directory `/home/c/testSvn2/trunk/packages/bowtie/trunk'
       make[1]: *** [override_dh_auto_build] Error 2
       make[1]: Leaving directory `/home/c/testSvn2/trunk/packages/bowtie/trunk'
       make: *** [build] Error 2
       dpkg-buildpackage: error: debian/rules build gave error exit status 2
       debuild: fatal error at line 1325:
       dpkg-buildpackage -rfakeroot -D -us -uc failed




For neobio, the following sequence works however:

being in trunk/packages/neobio/

c@n:~/testSvn2/trunk/packages/bowtie$ tar xzf
tarballs/neobio_0.0.20030929.orig.tar.gz
  cd neobio-0.0.20030929.orig/
  ln -s ../trunk/debian/ .
  fakeroot ./debian/rules
  fakeroot ./debian/rules binary

------------------------------------------------

>Do you mean something like
>MYVARIABLE := $(shell find . -name something )
Yes, but unfortunately it seems to work only in the preample of the rules file
but not after a target.
For example the following in rules produces an error:

override_dh_auto_build:
	echo override_dh_auto_build
	MYVARIABLE := $(shell find . -name something )

This yields the output
   ./debian/rules:16: *** commands commence before first target.  Stop.

Regards

Christoph