[Debian-med-packaging] [biopython] Building Debian jessie packages for 1.65 fails during tests (#540)

[Andreas Tille]

Hi,

On Sat, May 09, 2015 at 02:09:17AM -0700, Kai Blin wrote:
> Ok, with the following changes (apart from bumping the release numbers in debian/changelog), 1.65 builds in a jessie pbuilder for me:

One part of the patch was just commited this morning by me into
the packaging SVN.  However, the part marked below is just hiding
the problem by excluding the test:

> diff -ur debian.orig/rules debian/rules
> --- debian.orig/rules	2015-05-09 11:02:22.046561064 +0200
> +++ debian/rules	2015-05-09 10:53:02.555786699 +0200
> @@ -42,7 +42,7 @@
>  #        specifically since test_ColorSpiral and test_trie are running when called manually
>  #        .
>  #        Regarding the Tutorial test it depends from a fix for python-reportlab (see #745985)
> -EXCLUDEFAILINGTESTS=GenomeDiagram Fasttree_tool Mafft_tool Tutorial ColorSpiral trie
> +EXCLUDEFAILINGTESTS=GenomeDiagram Fasttree_tool Mafft_tool Tutorial ColorSpiral trie SeqIO_index

Here you simply exclude SeqIO_index which is the failing test - I'd
prefer to rather fix the test.
  
>  # FIXME: Currently it is not sure for what architecture samtools will be available
>  #        to anable a smooth migration to testing the build-dependency will be dropped
> @@ -86,8 +86,9 @@
>  	LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
>  		--test-args='set -e; \
>                               mkdir -p {build_dir}/home; \
> -                             mkdir -p {build_dir}/Doc; \
> +                             mkdir -p {build_dir}/Doc/examples/nmr; \
>                               cp -a Doc/Tutorial.tex {build_dir}/Doc; \
> +                             cp -a Doc/examples/nmr/noed.xpk {build_dir}/Doc/examples/nmr; \
>                               cp -a Tests {build_dir}; \

This is really needed to successfully run the test suite.

> So I remove a patch that is included in 1.65, I skip the wonky SeqIO_index test and I make sure the Debian build env has the `noed.xpk` file.
> @tillea, if you want that diff file, let me know how to best send it to you.

As I said I developed it this morning myself - at least the second part.

> If @peterjc can fix the SeqIO_index test, we could just patch that instead of skipping the whole test.

I'd be interested in a fix for SeqIO_index and I'd support Peters assumption
that it is connected to the fact that the test is running in the target dir
where the *.py files are moved to for beeing installed in the package.

Thanks for the patch anyway

      Andreas.

-- 
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