The GNUstep domain of some applications is possibly wrong: they are installed in the Local domain while this one is the equivalent of /usr/local, and so should be left untouched by the system package manager. The fix is to install them in the System domain. There might be a confusion because "System" leads to think that this domain is only for system tools (as in Mac OS X), but this is not the case. Quote from GNUstep documentation: The System domain is found in the `System' folder of the GNUstep installation. This directory contains all files which were included in the default GNUstep installation or distribution. Normally these include the basic GNUstep libraries (Foundation and AppKit), and might include essential system applications (the Workspace Manager, the Editor, applications related to system administrative tasks), the developer applications (Project Center and Gorm, as well as header files), essential extensions (bundles for XML, SSL, RTF, etc), as well as all software installed by the manufacturer of your distribution. While at first glance, the Local domain seems very similar to the System domain, there are several differences between them. The most important thing is the differing purpose of the Local domain, as it is meant as the location for installing software which was not included with your GNUstep distribution and which you or your local sysadmin compile and/or install manually. These may include third party applications, custom extension libraries and their related header files, etc. The Local domain is - as the name suggests - usually installed as `Local' on your GNUstep system. Every software (except for gnustep-make, gnustep-base, gnustep-gui and gnustep-back which by default install into the System domain) should install by default into the Local domain, so that if you download a source tarball of the software and you install it, it installs by default in the right place for this operation (the Local domain). Distributions should override this default manually when they package the software they want to distribute as part of their distribution, so that in that case the software is installed in the System domain. The ebuilds concerned by this are: gnustep-apps/gorm gnustep-apps/vindaloo gnustep-apps/cenon gnustep-apps/price gnustep-apps/addresses gnustep-apps/gridlock gnustep-apps/aclock gnustep-apps/cynthiune gnustep-apps/gmines gnustep-apps/projectmanager gnustep-apps/gnumail gnustep-apps/affiche gnustep-apps/stepulator gnustep-apps/talksoup gnustep-apps/mylibrary gnustep-apps/easydiff gnustep-libs/rigs gnustep-libs/camaelon gnustep-libs/popplerkit gnustep-libs/netclasses x11-wm/windowmaker Reproducible: Always
Updated ebuilds in the GNUstep overlay now all install in System (including most of those listed here, more to come later): http://overlays.gentoo.org/proj/gnustep/wiki
OK, packages from the overlay are arriving in portage What's left: gnustep-apps/gridlock gnustep-apps/stepulator gnustep-apps/easydiff gnustep-libs/rigs gnustep-libs/camaelon
This bug was finally fixed when new camaelon packages were added in portage All packages are fixed now, thanks for the bugreport!