I think this output pretty much says it all: kamil@allose:/usr/local/share $ equery belongs EMBOSS PHYLIPNEW [ Searching for file(s) EMBOSS,PHYLIPNEW in *... ] sci-biology/embassy-phylipnew-3.67 (/usr/local/share/EMBOSS) sci-biology/embassy-phylipnew-3.67 (/usr/local/share/PHYLIPNEW) sci-biology/embassy-iprscan-4.3.1 (/usr/local/share/EMBOSS) sci-biology/embassy-hmmer-2.3.2-r2 (/usr/local/share/EMBOSS) sci-biology/embassy-topo-1.0.0-r5 (/usr/local/share/EMBOSS) sci-biology/embassy-emnu-1.05-r5 (/usr/local/share/EMBOSS) sci-biology/embassy-esim4-1.0.0-r5 (/usr/local/share/EMBOSS) sci-biology/embassy-signature-0.1.0-r3 (/usr/local/share/EMBOSS) sci-biology/embassy-vienna-1.7.2 (/usr/local/share/EMBOSS) sci-biology/embassy-domsearch-0.1.0-r3 (/usr/local/share/EMBOSS) sci-biology/embassy-memenew-0.1.0-r1 (/usr/local/share/EMBOSS) sci-biology/embassy-mira-2.8.2 (/usr/local/share/EMBOSS) sci-biology/embassy-cbstools-1.0.0 (/usr/local/share/EMBOSS) sci-biology/embassy-structure-0.1.0-r3 (/usr/local/share/EMBOSS) sci-biology/embassy-mse-1.0.0-r6 (/usr/local/share/EMBOSS) sci-biology/embassy-domalign-0.1.0-r3 (/usr/local/share/EMBOSS) Worse yet, sci-biology/emboss which uses these packages expects them to be be in /usr/share/EMBOSS Reproducible: Always Steps to Reproduce:
Corrected eclass in CVS. Reinstalling affected packages should fix them. Thanks for reporting.