[Debian-med-packaging] Bug#937252: Asking for removal of pbalign (Was: Bug#937252: pbalign: Python2 removal in sid/bullseye)

[Andreas Tille]

Control: reassign -1 ftp.debian.org
Control: retitle -1 ROM: Please remove pbalign

Hi,

there are incompatibilities with latest pbcore and pbcommand:

pylint --errors-only pbalign
************* Module pbalign.pbalignrunner
pbalign/pbalignrunner.py:50:0: E0611: No name 'pbparser_runner' in module 'pbcommand.cli' (no-name-in-module)
************* Module pbalign.options
pbalign/options.py:40:0: E0611: No name 'get_pbparser' in module 'pbcommand.models' (no-name-in-module)
************* Module pbalign.alignservice.gmap
pbalign/alignservice/gmap.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)
pbalign/alignservice/gmap.py:40:0: E0401: Unable to import 'pbcore.util.Process' (import-error)
************* Module pbalign.alignservice.bowtie
pbalign/alignservice/bowtie.py:39:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)
pbalign/alignservice/bowtie.py:39:0: E0401: Unable to import 'pbcore.util.Process' (import-error)
************* Module pbalign.alignservice.fastabasedalign
pbalign/alignservice/fastabasedalign.py:40:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)
pbalign/alignservice/fastabasedalign.py:40:0: E0401: Unable to import 'pbcore.util.Process' (import-error)
************* Module pbalign.tasks.align_minorvariants
pbalign/tasks/align_minorvariants.py:9:0: E0611: No name 'get_pbparser' in module 'pbcommand.models' (no-name-in-module)
pbalign/tasks/align_minorvariants.py:10:0: E0611: No name 'pbparser_runner' in module 'pbcommand.cli' (no-name-in-module)
************* Module pbalign.utils.RgnH5IO
pbalign/utils/RgnH5IO.py:13:0: E0611: No name 'BasH5IO' in module 'pbcore.io' (no-name-in-module)
pbalign/utils/RgnH5IO.py:13:0: E0401: Unable to import 'pbcore.io.BasH5IO' (import-error)
pbalign/utils/RgnH5IO.py:56:0: E1126: Sequence index is not an int, slice, or instance with __index__ (invalid-sequence-index)
************* Module pbalign.utils.fileutil
pbalign/utils/fileutil.py:42:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)
pbalign/utils/fileutil.py:42:0: E0401: Unable to import 'pbcore.util.Process' (import-error)
************* Module pbalign.utils.progutil
pbalign/utils/progutil.py:37:0: E0611: No name 'Process' in module 'pbcore.util' (no-name-in-module)
pbalign/utils/progutil.py:37:0: E0401: Unable to import 'pbcore.util.Process' (import-error)
************* Module pbalign.tools.createChemistryHeader
pbalign/tools/createChemistryHeader.py:14:0: E0611: No name 'BasH5IO' in module 'pbcore.io' (no-name-in-module)
************* Module pbalign.tools.loadChemistry
pbalign/tools/loadChemistry.py:71:14: E0602: Undefined variable 'BasH5Reader' (undefined-variable)
************* Module pbalign.tools.mask_aligned_reads
pbalign/tools/mask_aligned_reads.py:12:0: E0611: No name 'CmpH5Reader' in module 'pbcore.io' (no-name-in-module)
pbalign/tools/mask_aligned_reads.py:12:0: E0611: No name 'EmptyCmpH5Error' in module 'pbcore.io' (no-name-in-module)
pbalign/tools/mask_aligned_reads.py:124:13: E1123: Unexpected keyword argument 'version' in constructor call (unexpected-keyword-arg)
make: *** [Makefile:19: pylint] Fehler 2


Issue tracker for https://github.com/PacificBiosciences/pbalign/ is disabled - so no idea how to ask for updates


Please remove pbalign from Debian.

Kind regards, Andreas.


-- 
http://fam-tille.de