rev-upgrade: Error opening or reading file

[kurt@…]

Maybe I'm doing something wrong here. I thought MacPorts automatically resolved dependencies, so I'm not sure why these errors are occurring. Is it a bug? Or something I'm doing (or not doing)? (Apologies if the latter.)

sudo port selfupdate
--->  Updating MacPorts base sources using rsync
MacPorts base version 2.1.2 installed,
MacPorts base version 2.1.2 downloaded.
--->  Updating the ports tree
--->  MacPorts base is already the latest version

The ports tree has been updated. To upgrade your installed ports, you should run
  port upgrade outdated
KBook:~ kurt$ sudo port install mysql5
--->  Computing dependencies for mysql5
--->  Cleaning mysql5
--->  Scanning binaries for linking errors: 34.3%
Warning: Error parsing file /Applications/MacPorts/AquaTerm.app/Contents/MacOS/AquaTerm: Error opening or reading file
--->  Scanning binaries for linking errors: 40.5%
Warning: Error parsing file /Applications/MacPorts/Python 2.7/Build Applet.app/Contents/MacOS/Python: Error opening or reading file
--->  Scanning binaries for linking errors: 40.7%
Warning: Error parsing file /Applications/MacPorts/Python 2.7/Python Launcher.app/Contents/MacOS/Python Launcher: Error opening or reading file
--->  Scanning binaries for linking errors: 75.5%
Warning: Error parsing file /opt/local/lib/mysql5/bin/innochecksum: Error opening or reading file
--->  Scanning binaries for linking errors: 75.7%
Warning: Error parsing file /opt/local/lib/mysql5/bin/my_print_defaults: Error opening or reading file
--->  Scanning binaries for linking errors: 75.8%
Warning: Error parsing file /opt/local/lib/mysql5/bin/myisam_ftdump: Error opening or reading file
--->  Scanning binaries for linking errors: 75.9%
Warning: Error parsing file /opt/local/lib/mysql5/bin/myisamchk: Error opening or reading file
--->  Scanning binaries for linking errors: 76.0%
Warning: Error parsing file /opt/local/lib/mysql5/bin/myisamlog: Error opening or reading file
--->  Scanning binaries for linking errors: 76.1%
Warning: Error parsing file /opt/local/lib/mysql5/bin/myisampack: Error opening or reading file
--->  Scanning binaries for linking errors: 76.2%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysql: Error opening or reading file
--->  Scanning binaries for linking errors: 76.3%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysql_client_test: Error opening or reading file
--->  Scanning binaries for linking errors: 76.5%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysql_client_test_embedded: Error opening or reading file
--->  Scanning binaries for linking errors: 76.6%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysql_tzinfo_to_sql: Error opening or reading file
--->  Scanning binaries for linking errors: 76.7%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysql_upgrade: Error opening or reading file
--->  Scanning binaries for linking errors: 76.8%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysql_waitpid: Error opening or reading file
--->  Scanning binaries for linking errors: 76.9%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqladmin: Error opening or reading file
--->  Scanning binaries for linking errors: 77.0%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqlbinlog: Error opening or reading file
--->  Scanning binaries for linking errors: 77.1%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqlcheck: Error opening or reading file
--->  Scanning binaries for linking errors: 77.3%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqldump: Error opening or reading file
--->  Scanning binaries for linking errors: 77.4%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqlimport: Error opening or reading file
--->  Scanning binaries for linking errors: 77.5%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqlshow: Error opening or reading file
--->  Scanning binaries for linking errors: 77.6%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqlslap: Error opening or reading file
--->  Scanning binaries for linking errors: 77.7%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqltest: Error opening or reading file
--->  Scanning binaries for linking errors: 77.8%
Warning: Error parsing file /opt/local/lib/mysql5/bin/mysqltest_embedded: Error opening or reading file
--->  Scanning binaries for linking errors: 77.9%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_config: Error opening or reading file
--->  Scanning binaries for linking errors: 78.1%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_delete_all: Error opening or reading file
--->  Scanning binaries for linking errors: 78.2%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_desc: Error opening or reading file
--->  Scanning binaries for linking errors: 78.3%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_drop_index: Error opening or reading file
--->  Scanning binaries for linking errors: 78.4%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_drop_table: Error opening or reading file
--->  Scanning binaries for linking errors: 78.5%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_mgm: Error opening or reading file
--->  Scanning binaries for linking errors: 78.6%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_print_backup_file: Error opening or reading file
--->  Scanning binaries for linking errors: 78.7%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_print_schema_file: Error opening or reading file
--->  Scanning binaries for linking errors: 78.9%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_print_sys_file: Error opening or reading file
--->  Scanning binaries for linking errors: 79.0%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_restore: Error opening or reading file
--->  Scanning binaries for linking errors: 79.1%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_select_all: Error opening or reading file
--->  Scanning binaries for linking errors: 79.2%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_select_count: Error opening or reading file
--->  Scanning binaries for linking errors: 79.3%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_show_tables: Error opening or reading file
--->  Scanning binaries for linking errors: 79.4%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_test_platform: Error opening or reading file
--->  Scanning binaries for linking errors: 79.5%
Warning: Error parsing file /opt/local/lib/mysql5/bin/ndb_waiter: Error opening or reading file
--->  Scanning binaries for linking errors: 79.7%
Warning: Error parsing file /opt/local/lib/mysql5/bin/perror: Error opening or reading file
--->  Scanning binaries for linking errors: 79.8%
Warning: Error parsing file /opt/local/lib/mysql5/bin/replace: Error opening or reading file
--->  Scanning binaries for linking errors: 79.9%
Warning: Error parsing file /opt/local/lib/mysql5/bin/resolve_stack_dump: Error opening or reading file
--->  Scanning binaries for linking errors: 80.0%
Warning: Error parsing file /opt/local/lib/mysql5/bin/resolveip: Error opening or reading file
--->  Scanning binaries for linking errors: 80.1%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/libmysqlclient.16.dylib: Error opening or reading file
--->  Scanning binaries for linking errors: 80.2%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/libmysqlclient_r.16.dylib: Error opening or reading file
--->  Scanning binaries for linking errors: 80.3%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/libndbclient.3.dylib: Error opening or reading file
--->  Scanning binaries for linking errors: 80.5%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/plugin/ha_example.0.so: Error opening or reading file
--->  Scanning binaries for linking errors: 80.6%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/plugin/ha_innodb_plugin.0.so: Error opening or reading file
--->  Scanning binaries for linking errors: 80.7%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/plugin/libdaemon_example.0.so: Error opening or reading file
--->  Scanning binaries for linking errors: 80.8%
Warning: Error parsing file /opt/local/lib/mysql5/mysql/plugin/mypluglib.0.so: Error opening or reading file
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.

[larryv (Lawrence Velázquez)]

Reformatted pasted port output.

[larryv (Lawrence Velázquez)]

Replying to kurt@…:

KBook:~ kurt$ sudo port install mysql5
--->  Computing dependencies for mysql5
--->  Cleaning mysql5
--->  Scanning binaries for linking errors: 34.3%

It doesn't look like mysql5 was actually installed by this command; it might have been present already. What is the output of port installed mysql\*?

[larryv (Lawrence Velázquez)]

Cc Me!

[ryandesign (Ryan Carsten Schmidt)]

Yes, mysql5 was already successfully installed before the commands you showed us.

After you install or upgrade any port, MacPorts then checks the linking of all ports, and reports any problems; this feature is called "rev-upgrade". In this case, no errors were reported ("No broken files found"). Several warnings were reported however, of which I don't quite know what to make. For any of the files where rev-upgrade said "Error opening or reading file" can you identify anything unusual about the file? Can you read it? Are its permissions ok?

[kurt@…]

Replying to larryv@…:

Replying to kurt@…:

KBook:~ kurt$ sudo port install mysql5
--->  Computing dependencies for mysql5
--->  Cleaning mysql5
--->  Scanning binaries for linking errors: 34.3%

It doesn't look like mysql5 was actually installed by this command; it might have been present already. What is the output of port installed mysql\*?

port installed mysql

None of the specified ports are installed.

[ryandesign (Ryan Carsten Schmidt)]

Correct, there is no port called "mysql". Try "port installed mysql\*" as Larry said. Or "port installed | grep mysql".

[kurt@…]

Replying to ryandesign@…:

Correct, there is no port called "mysql". Try "port installed mysql\*" as Larry said. Or "port installed | grep mysql".

Sorry about that

 port installed mysql\*
The following ports are currently installed:
  mysql5 @5.1.61_0
  mysql5 @5.1.62_0
  mysql5 @5.1.63_0
  mysql5 @5.1.66_2 (active)
  mysql5-server @5.1.61_0
  mysql5-server @5.1.62_0
  mysql5-server @5.1.63_0
  mysql5-server @5.1.66_1 (active)
  mysql51 @5.1.66_1 (active)
  mysql_select @0.1.2_0 (active)

Over the years, I have installed perl files from multiple sources: cpan, manual installation, macports. As a result, I was getting modules distributed in way too many directories. I actually uninstalled and reinstalled macports with the idea that I would try to put all the perl libs in the same tree making MacPorts my primary source of public perl libs. But I'm not getting very far.

When installing previous ports, MacPorts correctly identified dependencies and installed the appropriate files.

In looking at permissions, the owner/group of everything in /opt is root/admin with rwxr-xr-x permissions. The restricted write access might be a concern - except I'm using sudo to install with MacPorts, so permissions shouldn't be an issue (?)

[larryv (Lawrence Velázquez)]

Cc Me!

[ryandesign (Ryan Carsten Schmidt)]

rwxr-xr-x permissions on directories are normal.

So, what's going on here? Are you able to read any of the files rev-upgrade said it couldn't read? What's the output of, for example:

otool -L /opt/local/lib/mysql5/mysql/plugin/mypluglib.0.so

[neverpanic (Clemens Lang)]

7 months and no reply. Since we cannot reproduce the issue and haven't seen any other reports, closing as worksforme.