If boost is in USE, votca-tools uses the src votca-tools-1.2_pristine.tar.gz whereas with -boost it uses votca-tools-1.2.tar.gz. the _pristine tar extract to .../votca-tools-1.2/work/votca-tools-1.2_pristine but the ebuild expects $S to be .../votca-tools-1.2/work/votca-tools-1.2 which breaks the merge. The sequence: :; ebuild /usr/portage/sci-libs/votca-tools/votca-tools-1.2.ebuild unpack :; mv /var/tmp/portage/sci-libs/votca-tools-1.2/work/votca-tools-1.2_pristine /var/tmp/portage/sci-libs/votca-tools-1.2/work/votca-tools-1.2 :; ebuild /usr/portage/sci-libs/votca-tools/votca-tools-1.2.ebuild merge works, so the fix is either to set $S based on whether boost is set or to rename the extracted directory to s/_pristine//. Reproducible: Always Steps to Reproduce: 1. USE=boost emerge sci-libs/vocta-tools 2. 3.
Make no use of pristine tarball for now. Prefix dir in tarball was fixed upstream, so it will work in 1.2.1 again.