Bugzilla Bug 168043

Some notes on ROOT:

* The idea behind ROOT is that one can build a system with ROOT=/somewhere and
then chroot into it or tar up /somewhere as a system image. It is not designed
to allow the user to run /somewhere/usr/bin/foo.

* ROOT can't be used correctly in src_*, since ROOT might be different when
merging a binary package. For example, a binary package might be built with
ROOT=/ and then installed onto a system using ROOT=/somewhere.

* ROOT isn't used for library dependencies. When building, libraries, headers
etc. on / have to be used. Cross-compiling etc is done by configuring the
toolchain correctly, not by hacking ebuilds in a way that breaks binary
packages.

Summary of all mentioned herds:
  graphics kde sci sci-biology sci-chemistry

QA checks for package directory /sci-biology/trnascan-se:
/sci-biology/trnascan-se/trnascan-se-1.23-r1.ebuild
  21: sed -e "s%BINDIR  = \$(HOME)/bin%BINDIR = ${ROOT}/usr/bin%" \
  22: -e "s%LIBDIR  = \$(HOME)/lib/tRNAscan-SE%LIBDIR = ${ROOT}/usr/lib/${PN}%"
\
  23: -e "s%MANDIR  = \$(HOME)/man%MANDIR = ${ROOT}/usr/share/man%" \
herds: sci-biology

QA checks for package directory /sci-chemistry/caver:
/sci-chemistry/caver/caver-0.99.2.ebuild
  38: -e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \
/sci-chemistry/caver/caver-0.99.4.ebuild
  48: sed -e "s:^\(CAVER_BINARY_LOCATION\).*:\1 = \"${ROOT}usr/bin/caver\":g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/ccp4:
/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild
  250: -e "s:${S}:${ROOT}usr:g" \
  254: #                -e "s:${S}:${ROOT}usr:g" \
/sci-chemistry/ccp4/ccp4-6.0.2.ebuild
  220: -e "s:${S}:${ROOT}usr:g" \
  224: #                -e "s:${S}:${ROOT}usr:g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/cns:
/sci-chemistry/cns/cns-1.1.ebuild
  82: -e "s:${S}:${ROOT}usr:g" \
  83: -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${ROOT}usr:g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/coot:
/sci-chemistry/coot/coot-0.1.2.ebuild
  60: -e
"s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:${ROOT}usr/bin/probe:g"
\
  61: -e
"s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:${ROOT}usr/bin/reduce:g"
\
herds: sci-chemistry

QA checks for package directory /sci-chemistry/eden:
/sci-chemistry/eden/eden-5.3.ebuild
  27: -e "s:^\(FFTW.*=\).*:\1 ${ROOT}usr:g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/maxit:
/sci-chemistry/maxit/maxit-8.2.ebuild
  38: -e "s:^\(GINCLUDE=\).*:\1-I${ROOT}usr/include/rcsb:g" \
  39: -e "s:^\(LIBDIR=\).*:\1${ROOT}usr/$(get_libdir):g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/pdb-extract:
/sci-chemistry/pdb-extract/pdb-extract-1.700.ebuild
  34: -e "s:^\(GINCLUDE=\).*:\1-I${ROOT}usr/include/rcsb:g" \
  35: -e "s:^\(LIBDIR=\).*:\1${ROOT}usr/$(get_libdir):g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/shelx:
/sci-chemistry/shelx/shelx-20060317.ebuild
  37: -e "s:CIFDIR='/usr/local/bin/':CIFDIR='${ROOT}usr/share/${PN}/':g" \
herds: sci-chemistry

QA checks for package directory /sci-chemistry/sparky:
/sci-chemistry/sparky/sparky-3.111.ebuild
  67: -e "s:^\(set PYTHON[[:space:]]*=\).*:\1 ${ROOT}usr/bin/python${PYVER}:g"
\
  68: -e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${ROOT}usr/$(get_libdir):g"
\
herds: sci-chemistry

QA checks for package directory /sci-chemistry/validation:
/sci-chemistry/validation/validation-6.2.ebuild
  37: -e "s:^\(GINCLUDE=\).*:\1-I${ROOT}usr/include/rcsb:g" \
  38: -e "s:^\(LIBDIR=\).*:\1${ROOT}usr/$(get_libdir):g" \
herds: sci-chemistry

QA checks for package directory /sci-libs/coot-data:
/sci-libs/coot-data/coot-data-1.ebuild
  28: COOT_REFMAC_LIB_DIR="${ROOT}usr/share/coot/lib"
herds: sci-chemistry

QA checks for package directory /sci-libs/rcsb-data:
/sci-libs/rcsb-data/rcsb-data-1.700.ebuild
  25: -e "s:^\(BINDIR=\).*:\1${ROOT}usr/bin:g" \
herds: sci-chemistry

QA checks for package directory /sci-visualization/grace:
/sci-visualization/grace/grace-5.1.20.ebuild
  54: sed -i -e "s%doc/%${ROOT}usr/share/doc/${PF}/html/%g" src/*
  55: sed -i -e "s%examples/%${ROOT}usr/share/doc/${PF}/examples/%g"
src/xmgrace.c
herds: graphics, sci

QA checks for package directory /sci-visualization/labplot:
/sci-visualization/labplot/labplot-1.5.1.3.ebuild
  52: export QTDIR="${ROOT}/usr/qt/3"
  53: export QWT3D_PATH="${ROOT}/usr"
  54: export KEXIDB_DIR="${ROOT}/usr"
/sci-visualization/labplot/labplot-1.5.1.4.ebuild
  52: export QTDIR="${ROOT}/usr/qt/3"
  53: export QWT3D_PATH="${ROOT}/usr"
  54: export KEXIDB_DIR="${ROOT}/usr"
herds: kde, sci

fixed all of them.