Re: Issues to build latest spades
On 11/12/19 7:59 PM, Andreas Tille wrote:
> 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'
in python3, there is no more iteritems, should use .items()
Olivier
>
>
> == Error == exception caught: <class 'AttributeError'>
>
> In case you have troubles running SPAdes, you can write to spades.support@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.
>
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
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