[MacPorts] #32686: Registry DB corrupted after selfupdate

[MacPorts]

#32686: Registry DB corrupted after selfupdate
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 Reporter:  falkschramm@…          |       Owner:  macports-tickets@…                   
     Type:  defect                 |      Status:  new                                  
 Priority:  Normal                 |   Milestone:                                       
Component:  base                   |     Version:  2.0.3                                
 Keywords:                         |        Port:                                       
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Comment(by stephen@…):

 ports tree (including base) at r88772 here, port last built 8 minutes ago,
 and
 {{{
 MacPorts 21:40$ sudo port version
 Password:
 sqlite error: SQL logic error or missing database (1) while executing
 query: COMMIT
     while executing
 "registry::open $db_path"
     (procedure "mportinit" line 578)
     invoked from within
 "mportinit ui_options global_options global_variations"
 Error: /opt/local/bin/port: Failed to initialize MacPorts, sqlite error:
 SQL logic error or missing database (1) while executing query: COMMIT
 }}}
 So I don't think the fix in r88411 is related to this.

 {{{/opt/local/var/macports/registry/registry.db-journal}}} exists and has
 permissions "-rw-r--r--  1 root  admin" with size 7176 and date Jan 11
 23:32 JST (ie, about the same as the build time).
 {{{/opt/local/var/macports/registry/registry.db}}} exists and has
 permissions "-rw-r--r--  1 root  admin" with size 76739584 and the same
 time.

 I also have a broken port, py25-wxpython (see ticket #32700), which is
 from about two weeks ago.

 Why does {{{port}}} need to open the registry to give its version?

 Following the thread described by pixilla, I ran the integrity check:
 {{{
 wideload:MacPorts/base 0:01$ sudo sqlite3
 SQLite version 3.7.9 2011-11-01 00:52:41
 sqlite> attach database "/opt/local/var/macports/registry/registry.db" as
 registry;
 sqlite> .load /Users/steve/src/MacPorts/base/src/cregistry/macports.sqlext
 sqlite> pragma integrity_check;
 rowid 45024 missing from index file_path
 rowid 138844 missing from index file_actual
 sqlite> .quit
 }}}

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Ticket URL: <https://trac.macports.org/ticket/32686#comment:11>
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