The ebuild probably needs some tweaks. I am not familiar with the installation process of repeatmasker but I wonder what is going on. I will post the full emerge output. However, things to watch: 1. cross_match path is not set: Enter path [ /var/tmp/portage/sci-biology/repeatmasker-3.2.7/work/RepeatMasker ]: -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-3.2.7/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory 2. trf symlink is not detected? **TRF INSTALLATION PATH** This is the path to the location where the TRF program can be found. This is used by the RepeatProteinMask program. [NOTE: This script assumes the trf program is called "trf". If it is name trf###-linux.exe you will need to create a symlink called "trf" to it or rename it first. Enter path [ ]: $ equery files trf * Searching for trf ... * Contents of sci-biology/trf-4.0: /opt /opt/trf /opt/trf/trf400.linux.exe /usr /usr/bin /usr/bin/trf -> /opt/trf/trf400.linux.exe $ Weird. How can I figure out what is configured in repeatmasker and what's not? Reading the FAQ on their site did not help. :(
Created attachment 201287 [details] emerge output
This output is normal and a result of piping a batch of replies to a script that's supposed to be interactive. If you're having any trouble emerging or running the program, please file a bug about that.
To see the code responsible for this output, check the configure script in the RepeatMasker tarball and the relevant portion of the ebuild.
