cgit @0.9.0.3_0 Warning: Violation by /usr -- Warning: cgit violates the layout of the ports-filesystems!

[peter.hillerstrom+macports@…]

When doing port -u upgrade outdated, I noticed an error in cgit port:

--->  Computing dependencies for cgit
--->  Fetching archive for cgit
--->  Attempting to fetch cgit-0.9.0.3_0.darwin_10.x86_64.tbz2 from http://lil.fr.packages.macports.org/cgit
--->  Attempting to fetch cgit-0.9.0.3_0.darwin_10.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/cgit
--->  Attempting to fetch cgit-0.9.0.3_0.darwin_10.x86_64.tbz2 from http://packages.macports.org/cgit
--->  Fetching distfiles for cgit
--->  Attempting to fetch cgit-0.9.0.3.tar.bz2 from http://lil.fr.distfiles.macports.org/git-core
--->  Attempting to fetch git-1.7.4.tar.bz2 from http://lil.fr.distfiles.macports.org/git-core
--->  Verifying checksum(s) for cgit
--->  Extracting cgit
--->  Configuring cgit
--->  Building cgit
--->  Staging cgit into destroot
Warning: violation by /usr
Warning: cgit violates the layout of the ports-filesystems!
Warning: Please fix or indicate this misbehavior (if it is intended), it will be an error in future releases!
--->  Installing cgit @0.9.0.3_0
--->  Cleaning cgit
--->  Computing dependencies for cgit
--->  Deactivating cgit @0.8.2.1_1
--->  Cleaning cgit
--->  Activating cgit @0.9.0.3_0
--->  Cleaning cgit
--->  Uninstalling cgit @0.8.2.1_1
Error: org.macports.uninstall for port cgit returned: error deleting "/opt/local/var/macports/software/cgit/0.8.2.1_1": directory not empty
Please see the log file for port cgit for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_cgit_0.8.2.1_1/cgit/main.log
Warning: Failed to execute portfile from registry for cgit @0.8.2.1_1
--->  Uninstalling cgit @0.8.2.1_1
Error: Uninstall cgit @0.8.2.1_1 failed: error deleting "/opt/local/var/macports/software/cgit/0.8.2.1_1": directory not empty
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
91-157-48-10# port contents cgit
Port cgit contains:
  /opt/local/etc/cgitrc.sample
  /opt/local/var/cache/cgit/.turd_cgit
  /opt/local/www/data/cgit/cgit.cgi
  /opt/local/www/data/cgit/cgit.css
  /opt/local/www/data/cgit/cgit.png
  /usr/lib/cgit/filters/commit-links.sh
  /usr/lib/cgit/filters/syntax-highlighting.sh
91-157-48-10# port contents cgit@0.9.0.3_0        
Port cgit contains:
  /opt/local/etc/cgitrc.sample
  /opt/local/var/cache/cgit/.turd_cgit
  /opt/local/www/data/cgit/cgit.cgi
  /opt/local/www/data/cgit/cgit.css
  /opt/local/www/data/cgit/cgit.png
  /usr/lib/cgit/filters/commit-links.sh
  /usr/lib/cgit/filters/syntax-highlighting.sh
91-157-48-10# port contents cgit@0.8.2.1_1
Port cgit contains:
  /opt/local/etc/cgitrc.sample
  /opt/local/var/cache/cgit/.turd_cgit
  /opt/local/www/data/cgit/cgit.cgi
  /opt/local/www/data/cgit/cgit.css
  /opt/local/www/data/cgit/cgit.png
  /usr/lib/cgit/filters/commit-links.sh
  /usr/lib/cgit/filters/syntax-highlighting.sh

[peter.hillerstrom+macports@…]

Cc Me!

[ryandesign (Ryan Carsten Schmidt)]

Error: org.macports.uninstall for port cgit returned: error deleting "/opt/local/var/macports/software/cgit/0.8.2.1_1": directory not empty

This directory must be leftover from an old version of MacPorts (before the images-and-archives branch was merged—#19458). You can safely delete it manually.

Warning: violation by /usr

I can confirm this, and this needs to be fixed.

[jmroot (Joshua Root)]

The image directory should have been converted to an archive when you upgraded base. Try:

sudo port -df selfupdate

[peter.hillerstrom+macports@…]

Thank you!!! I think I finally got my ports installation fixed. I've been manually removing those directories.
Now they are all deleted and the selfupdate finished without problems.