Package: spades Version: 3.15.4+dfsg-1 Severity: normal Dear Maintainer,
Using spades with the --careful flag triggers the following error: Traceback (most recent call last): File "/usr/libexec/spades/spades.py", line 683, in <module> main(sys.argv) File "/usr/libexec/spades/spades.py", line 621, in main cfg, dataset_data, command_line = parse_args(args, log) File "/usr/libexec/spades/spades.py", line 257, in parse_args options, cfg, dataset_data = options_parser.parse_args(log, bin_home, spades_home, File "/usr/share/spades/spades_pipeline/options_parser.py", line 1157, in parse_args add_to_cfg(cfg, log, bin_home, spades_home, options_storage.args) File "/usr/share/spades/spades_pipeline/options_parser.py", line 995, in add_to_cfg if which("bwa-spades"): NameError: name 'which' is not defined Reproducible with e.g.: f="$(mktemp XXXX.fq)" echo -e "@a\nA\n+\n!" > "$f" spades --careful --12 "$f" -o "/tmp" The code path related to that flag in options_parser.py has been patched in Debian to add the call to which(): https://salsa.debian.org/med-team/spades/-/blob/d3c54b2ae8f0ee29a639fe0246d670fcad54b45b/debian/patches/0003_accept-system-bwa.patch#L82-L95 When the patch was initially created in this commit: https://salsa.debian.org/med-team/spades/-/commit/ac1cfa145bf4066ca7f3af47db1aae6dd28ac5ab the call and definition of which() were both in spades.py but the call was later moved to options_parser.py while the definition was left behind unused. Rather than adding multiple definitions of which() in the patch, the single version in support.py could be imported wherever it needs to be used. -- System Information: Debian Release: bookworm/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.17.0-1-amd64 (SMP w/4 CPU threads; PREEMPT) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages spades depends on: ii bamtools 2.5.1+dfsg-10+b1 ii bwa 0.7.17-7 ii libc6 2.33-7 ii libgcc-s1 12.1.0-1 ii libgomp1 12.1.0-1 ii libnlopt0 2.7.1-4+b1 ii libssw0 1.1-13 ii libstdc++6 12.1.0-1 ii python3 3.10.4-1+b1 ii python3-distutils 3.9.12-1 ii python3-joblib 0.17.0-4 ii python3-yaml 5.4.1-1+b1 ii samtools 1.13-4 ii zlib1g 1:1.2.11.dfsg-4 spades recommends no packages. spades suggests no packages. -- no debconf information