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.supp...@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 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438