Seems the USE flags interpretation is not correct. In package.use I have: sci-biology/emboss -pdf -png -X -mysql minimal static-libs but during emerge I see: >>> Emerging (1 of 1) sci-biology/emboss-6.6.0::gentoo * EMBOSS-6.6.0.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking EMBOSS-6.6.0.tar.gz to /var/tmp/portage/sci-biology/emboss-6.6.0/work >>> Source unpacked in /var/tmp/portage/sci-biology/emboss-6.6.0/work >>> Preparing source in /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0 ... * Applying emboss-6.6.0_fix-build-system.patch ... [ ok ] * Applying emboss-6.6.0_FORTIFY_SOURCE-fix.patch ... [ ok ] * Applying emboss-6.6.0_plplot-declarations.patch ... [ ok ] * Applying emboss-6.6.0_qa-implicit-declarations.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0' ... * Running libtoolize --install --copy --force --automake ... [ ok ] * Running aclocal -I m4 ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: EMBOSS-6.6.0/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/emboss-6.6.0/work/emboss-6.6.0_build" * econf: updating EMBOSS-6.6.0/config.guess with /usr/share/gnuconfig/config.guess * econf: updating EMBOSS-6.6.0/config.sub with /usr/share/gnuconfig/config.sub /var/tmp/portage/sci-biology/emboss-6.6.0/work/EMBOSS-6.6.0/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/emboss-6.6.0 --enable-shared --enable-static --without-x --without-pngdriver --without-hpdf --without-mysql --without-postgresql --enable-large --without-java --enable-systemlibs Note "--enable-shared --enable-static" above.
static-libs does not turn off shared libraries in Gentoo unless there is a good reason. Then it would be a flag of it's own.