[Debian-med-packaging] Bug#938521: Issues to build latest spades

[Andreas Tille]

Hi,

I've updated unicycler in Git.  When running the autopkgtest I get
an issue with spades.  So I went on to spades trying hard to build
its latest version but I was running into:

...
== Running assembler: K21

'dict' object has no attribute 'iteritems'
Traceback (most recent call last):
  File "/build/spades-3.13.1/install_spades/bin/spades.py", line 901, in main
    used_K = spades_logic.run_spades(tmp_configs_dir, bin_home, spades_cfg, dataset_data, ext_python_modules_home, log)
  File "/build/spades-3.13.1/install_spades/../../share/spades/spades_pipeline/spades_logic.py", line 334, in run_spades
    run_iteration(configs_dir, execution_home, cfg, log, K, None, False)
  File "/build/spades-3.13.1/install_spades/../../share/spades/spades_pipeline/spades_logic.py", line 217, in run_iteration
    for src, target in list(replacements.iteritems()):
AttributeError: 'dict' object has no attribute 'iteritems'


== Error ==  exception caught: <class 'AttributeError'>

In case you have troubles running SPAdes, you can write to spades.support at cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
/build/spades-3.13.1/install_spades/bin/spades.py:872: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))
make[1]: *** [debian/rules:61: override_dh_auto_test] Error 1



Please note: In commit 54bc9d00e8638f0ab350c620e9b5446f776340e7
I tried to address exactly this issue but failed obviously.

Any help would be really appreciated.

Kind regards

      Andreas.


-- 
http://fam-tille.de