[Debian-med-packaging] Bug#1120035: libbio-db-seqfeature-perl: Column name offset is a reserved word in MariaDB (>10.6)

[Moritz Schlarb]

Source: libbio-db-seqfeature-perl
Version: 1.7.5-1
Severity: important
Tags: upstream
Forwarded: https://github.com/bioperl/bio-db-seqfeature/issues/5
X-Debbugs-Cc: andresen at uni-mainz.de

Dear Maintainers,

when running the script bp_seqfeature_load on Bookworm or Trixie, we get

DBD::MariaDB::db do failed: You have an error in your SQL syntax; check the
manual that corresponds to your MariaDB server version for the right syntax to
use near 'offset   int(10) unsigned not null,
  sequence longblob,
  primary key(id,off...' at line 3 at
/usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm line 475.

-------------------- EXCEPTION --------------------
MSG: You have an error in your SQL syntax; check the manual that corresponds to
your MariaDB server version for the right syntax to use near 'offset   int(10)
unsigned not null,
  sequence longblob,
  primary key(id,off...' at line 3
STACK Bio::DB::SeqFeature::Store::DBI::MariaDB::_create_table
/usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm:475
STACK Bio::DB::SeqFeature::Store::DBI::MariaDB::_init_database
/usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm:448
STACK Bio::DB::SeqFeature::Store::init_database
/usr/share/perl5/Bio/DB/SeqFeature/Store.pm:426
STACK Bio::DB::SeqFeature::Store::DBI::MariaDB::init
/usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm:229
STACK Bio::DB::SeqFeature::Store::new
/usr/share/perl5/Bio/DB/SeqFeature/Store.pm:388
STACK toplevel /usr/bin/bp_seqfeature_load:237
-------------------------------------------

The reason for this is that offset is a reserved keyword since MariaDB 10.6
(cf. https://mariadb.com/docs/server/reference/sql-structure/sql-language-
structure/reserved-words).

Regards,
Moritz Schlarb


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