Your message dated Fri, 7 May 2021 09:58:25 +0200
with message-id <[email protected]>
and subject line Close bug
has caused the Debian Bug report #987044,
regarding libbiosig3: certain files can crash save2gdf and produce invalid json
output
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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987044: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=987044
Debian Bug Tracking System
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--- Begin Message ---
Package: libbiosig3
Version: 2.1.2-3
Severity: important
Tags: patch
Dear Maintainer,
as suggested by you [1], I'm filing this bug report.
* What led up to the situation?
Trying to handle this files
https://www.physionet.org/files/sleep-edfx/1.0.0/sleep-cassette/SC4001EC-Hypnogram.edf?download
with Biosig-tools causes these two issues :
1) save2gdf -JSON SC4001EC-Hypnogram.edf
fails to produce valid JSON, because it contains the field
SampleRate : inf
You can check with
save2gdf -JSON SC4001EC-Hypnogram.edf | json_pp
or python
import biosig, json
HDR = json.loads(biosig.header('SC4001EC-Hypnogram.edf'))
2) Converting the edf into a gdf file crashes. You can test with:
save2gdf SC4001EC-Hypnogram.edf SC4001EC-Hypnogram.edf.gdf
and does not produce the expected output.
* What exactly did you do (or not do) that was effective (or
ineffective)?
The patch as suggested [1] solves both issues, and a similar issue for
other file formats (ACQ, BKR, and HEKA).
The issue was most likely introduced in Jan 2018, when the initial read
page size was increased from 512 to 4096 bytes.
It most likely affects also libbiosig2 (v1.9.3) in buster.
Moreover, it might also affect the package Stimfit, which uses an
outdated copy of libbbiosig.
The best solution would be to rebuild stimfit with
./configure --with-biosig ...
or
./configure --with-biosig2 ...
with a build-dependency on libbiosig-dev, and a runtime dependency on
libbiosig2 | libbiosig3
The patches are already in upstream (see Jan 2021 in [2]);
The package sigviewer is also affected but updating libbiosig is
sufficient there because it is dynamically linked, and the API did not
change.
[1]
https://alioth-lists.debian.net/pipermail/debian-med-packaging/2021-April/091120.html
[2] https://github.com/neurodroid/stimfit/commits/master
Cheers,
Alois
--- End Message ---
--- Begin Message ---
Closing this bug since it is fixed in 2.1.2-4
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http://fam-tille.de
--- End Message ---
