| 1 |
jlec 12/08/31 07:41:17 |
| 2 |
|
| 3 |
Modified: ChangeLog |
| 4 |
Added: ccp4-apps-6.1.3-r11.ebuild |
| 5 |
Removed: ccp4-apps-6.1.3-r10.ebuild |
| 6 |
Log: |
| 7 |
sci-chemistry/ccp4-apps: Rename all manpages in order to avoid conflicts with other packages, #429410 |
| 8 |
|
| 9 |
(Portage version: 2.2.0_alpha123/cvs/Linux x86_64, RepoMan options: --force) |
| 10 |
|
| 11 |
Revision Changes Path |
| 12 |
1.38 sci-chemistry/ccp4-apps/ChangeLog |
| 13 |
|
| 14 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?rev=1.38&view=markup |
| 15 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?rev=1.38&content-type=text/plain |
| 16 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog?r1=1.37&r2=1.38 |
| 17 |
|
| 18 |
Index: ChangeLog |
| 19 |
=================================================================== |
| 20 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v |
| 21 |
retrieving revision 1.37 |
| 22 |
retrieving revision 1.38 |
| 23 |
diff -u -r1.37 -r1.38 |
| 24 |
--- ChangeLog 1 Jun 2012 09:06:21 -0000 1.37 |
| 25 |
+++ ChangeLog 31 Aug 2012 07:41:17 -0000 1.38 |
| 26 |
@@ -1,6 +1,12 @@ |
| 27 |
# ChangeLog for sci-chemistry/ccp4-apps |
| 28 |
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 |
| 29 |
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.37 2012/06/01 09:06:21 jlec Exp $ |
| 30 |
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.38 2012/08/31 07:41:17 jlec Exp $ |
| 31 |
+ |
| 32 |
+*ccp4-apps-6.1.3-r11 (31 Aug 2012) |
| 33 |
+ |
| 34 |
+ 31 Aug 2012; Justin Lecher <jlec@g.o> -ccp4-apps-6.1.3-r10.ebuild, |
| 35 |
+ +ccp4-apps-6.1.3-r11.ebuild: |
| 36 |
+ Rename all manpages in order to avoid conflicts with other packages, #429410 |
| 37 |
|
| 38 |
01 Jun 2012; Justin Lecher <jlec@g.o> files/6.1.3-lapack.patch, |
| 39 |
ccp4-apps-6.1.3-r10.ebuild: |
| 40 |
|
| 41 |
|
| 42 |
|
| 43 |
1.1 sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild |
| 44 |
|
| 45 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild?rev=1.1&view=markup |
| 46 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild?rev=1.1&content-type=text/plain |
| 47 |
|
| 48 |
Index: ccp4-apps-6.1.3-r11.ebuild |
| 49 |
=================================================================== |
| 50 |
# Copyright 1999-2012 Gentoo Foundation |
| 51 |
# Distributed under the terms of the GNU General Public License v2 |
| 52 |
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r11.ebuild,v 1.1 2012/08/31 07:41:17 jlec Exp $ |
| 53 |
|
| 54 |
EAPI=3 |
| 55 |
|
| 56 |
PYTHON_DEPEND="2" |
| 57 |
|
| 58 |
inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs |
| 59 |
|
| 60 |
MY_P="${PN/-apps}-${PV}" |
| 61 |
|
| 62 |
#UPDATE="04_03_09" |
| 63 |
#PATCHDATE="090511" |
| 64 |
|
| 65 |
PATCH_TOT="0" |
| 66 |
|
| 67 |
DESCRIPTION="Protein X-ray crystallography toolkit" |
| 68 |
HOMEPAGE="http://www.ccp4.ac.uk/" |
| 69 |
SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
| 70 |
SRC_URI=" |
| 71 |
${SRC}/${PV}/${MY_P}-core-src.tar.gz |
| 72 |
http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" |
| 73 |
# patch tarball from upstream |
| 74 |
[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
| 75 |
# patches created by us |
| 76 |
[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
| 77 |
|
| 78 |
for i in $(seq $PATCH_TOT); do |
| 79 |
NAME="PATCH${i}[1]" |
| 80 |
SRC_URI="${SRC_URI} |
| 81 |
${SRC}/${PV}/patches/${!NAME}" |
| 82 |
done |
| 83 |
|
| 84 |
LICENSE="ccp4" |
| 85 |
SLOT="0" |
| 86 |
KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" |
| 87 |
IUSE="examples X" |
| 88 |
|
| 89 |
X11DEPS=" |
| 90 |
x11-libs/libX11 |
| 91 |
x11-libs/libXaw |
| 92 |
x11-libs/libXt |
| 93 |
x11-libs/libxdl_view" |
| 94 |
|
| 95 |
TKDEPS=" |
| 96 |
>=dev-lang/tk-8.3 |
| 97 |
>=dev-tcltk/blt-2.4 |
| 98 |
dev-tcltk/iwidgets |
| 99 |
dev-tcltk/itcl |
| 100 |
dev-tcltk/itk |
| 101 |
>=dev-tcltk/tdom-0.8 |
| 102 |
dev-tcltk/tktreectrl" |
| 103 |
|
| 104 |
SCILIBS=" |
| 105 |
~sci-libs/ccp4-libs-${PV} |
| 106 |
>=sci-libs/ccp4-libs-${PV}-r7 |
| 107 |
sci-libs/clipper |
| 108 |
sci-libs/fftw:2.1 |
| 109 |
sci-libs/mmdb |
| 110 |
sci-libs/ssm |
| 111 |
virtual/blas |
| 112 |
virtual/lapack" |
| 113 |
|
| 114 |
SCIAPPS=" |
| 115 |
sci-chemistry/pdb-extract |
| 116 |
sci-chemistry/pymol |
| 117 |
sci-chemistry/rasmol |
| 118 |
>=sci-chemistry/oasis-4.0-r1" |
| 119 |
|
| 120 |
RDEPEND=" |
| 121 |
${TKDEPS} |
| 122 |
${SCILIBS} |
| 123 |
app-shells/tcsh |
| 124 |
dev-python/pyxml |
| 125 |
dev-libs/libxml2:2 |
| 126 |
dev-libs/libjwc_c |
| 127 |
dev-libs/libjwc_f |
| 128 |
dev-libs/boehm-gc |
| 129 |
virtual/fortran |
| 130 |
!app-office/sc |
| 131 |
!<sci-chemistry/ccp4-6.1.3 |
| 132 |
X? ( ${X11DEPS} )" |
| 133 |
DEPEND="${RDEPEND} |
| 134 |
X? ( |
| 135 |
x11-misc/imake |
| 136 |
x11-proto/inputproto |
| 137 |
x11-proto/xextproto |
| 138 |
)" |
| 139 |
PDEPEND="${SCIAPPS}" |
| 140 |
|
| 141 |
RESTRICT="mirror" |
| 142 |
|
| 143 |
S="${WORKDIR}/${MY_P}" |
| 144 |
|
| 145 |
pkg_setup() { |
| 146 |
fortran-2_pkg_setup |
| 147 |
python_set_active_version 2 |
| 148 |
} |
| 149 |
|
| 150 |
src_prepare() { |
| 151 |
einfo "Applying upstream patches ..." |
| 152 |
for patch in $(seq $PATCH_TOT); do |
| 153 |
base="PATCH${patch}" |
| 154 |
dir=$(eval echo \${${base}[0]}) |
| 155 |
p=$(eval echo \${${base}[1]}) |
| 156 |
pushd "${dir}" >& /dev/null |
| 157 |
ccp_patch "${DISTDIR}/${p}" |
| 158 |
popd >& /dev/null |
| 159 |
done |
| 160 |
einfo "Done." |
| 161 |
echo |
| 162 |
|
| 163 |
[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
| 164 |
|
| 165 |
einfo "Applying Gentoo patches ..." |
| 166 |
|
| 167 |
# it tries to create libdir, bindir etc on live system in configure |
| 168 |
ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
| 169 |
|
| 170 |
# We already have sci-chemistry/rasmol |
| 171 |
# Also remember to create the bindir. |
| 172 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch |
| 173 |
|
| 174 |
# libraries come from sci-libs/ccp4-libs |
| 175 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch |
| 176 |
|
| 177 |
# We have seperate ebuilds for those |
| 178 |
for bin in molref xia scala imosflm balbes; do |
| 179 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch |
| 180 |
done |
| 181 |
|
| 182 |
# don't configure what is not build |
| 183 |
ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch |
| 184 |
|
| 185 |
# Set python paths correctly |
| 186 |
ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch |
| 187 |
|
| 188 |
# Set python paths correctly |
| 189 |
ccp_patch "${FILESDIR}"/${PV}-pisa.patch |
| 190 |
|
| 191 |
# Set python paths correctly |
| 192 |
ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch |
| 193 |
|
| 194 |
# Fix upstreams code |
| 195 |
ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch |
| 196 |
|
| 197 |
# Not renaming, but unbundling libs |
| 198 |
ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch |
| 199 |
|
| 200 |
# Use pkg-config to detect BLAS/LAPCK |
| 201 |
ccp_patch "${FILESDIR}"/${PV}-lapack.patch |
| 202 |
|
| 203 |
# Update things for oasis 4 usage |
| 204 |
epatch "${WORKDIR}"/${PV}-oasis4.0.patch |
| 205 |
sed 's: oasis : :g' -i src/Makefile.in || die |
| 206 |
|
| 207 |
# unbundle libs |
| 208 |
ccp_patch "${FILESDIR}"/${PV}-unbundle.patch |
| 209 |
|
| 210 |
einfo "Done." # done applying Gentoo patches |
| 211 |
echo |
| 212 |
|
| 213 |
find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete |
| 214 |
|
| 215 |
sed \ |
| 216 |
-e "s:/usr:${EPREFIX}/usr:g" \ |
| 217 |
-e 's:-Wl,-rpath,$CLIB::g' \ |
| 218 |
-e 's: -rpath $CLIB::g' \ |
| 219 |
-e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
| 220 |
-e 's:sleep 1:sleep .2:g' \ |
| 221 |
-e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ |
| 222 |
-e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ |
| 223 |
-e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ |
| 224 |
-e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ |
| 225 |
-i configure || die |
| 226 |
|
| 227 |
sed \ |
| 228 |
-e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ |
| 229 |
-i src/Makefile* || die |
| 230 |
|
| 231 |
find "${S}" -name "Makefile.*" \ |
| 232 |
-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; |
| 233 |
|
| 234 |
# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version |
| 235 |
sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die |
| 236 |
|
| 237 |
# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. |
| 238 |
pushd src/rapper 2>/dev/null |
| 239 |
eautoreconf |
| 240 |
popd 2>/dev/null |
| 241 |
|
| 242 |
gnuconfig_update |
| 243 |
|
| 244 |
python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py |
| 245 |
} |
| 246 |
|
| 247 |
src_configure() { |
| 248 |
# Build system is broken if we set LDFLAGS |
| 249 |
export GENTOOLDFLAGS="${LDFLAGS}" |
| 250 |
unset LDFLAGS |
| 251 |
|
| 252 |
# These are broken with ./src/procheck/ps.f |
| 253 |
filter-flags "-floop-*" |
| 254 |
|
| 255 |
# GENTOO_OSNAME can be one of: |
| 256 |
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
| 257 |
# linux_compaq_compilers linux_intel_compilers generic Darwin |
| 258 |
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
| 259 |
if [[ "$(tc-getFC)" = "ifort" ]]; then |
| 260 |
if use ia64; then |
| 261 |
GENTOO_OSNAME="ia64_linux_intel" |
| 262 |
else |
| 263 |
# Should be valid for x86, maybe amd64 |
| 264 |
GENTOO_OSNAME="linux_intel_compilers" |
| 265 |
fi |
| 266 |
else |
| 267 |
# Should be valid for x86 and amd64, at least |
| 268 |
GENTOO_OSNAME="linux" |
| 269 |
fi |
| 270 |
|
| 271 |
# Sets up env |
| 272 |
ln -s \ |
| 273 |
ccp4.setup-bash \ |
| 274 |
"${S}"/include/ccp4.setup |
| 275 |
|
| 276 |
# We agree to the license by emerging this, set in LICENSE |
| 277 |
sed -i \ |
| 278 |
-e "s~^\(^agreed=\).*~\1yes~g" \ |
| 279 |
"${S}"/configure || die |
| 280 |
|
| 281 |
# Fix up variables -- need to reset CCP4_MASTER at install-time |
| 282 |
sed -i \ |
| 283 |
-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
| 284 |
-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ |
| 285 |
-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
| 286 |
-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ |
| 287 |
-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
| 288 |
"${S}"/include/ccp4.setup* || die |
| 289 |
|
| 290 |
# Set up variables for build |
| 291 |
source "${S}"/include/ccp4.setup-sh |
| 292 |
|
| 293 |
export CC=$(tc-getCC) |
| 294 |
export CXX=$(tc-getCXX) |
| 295 |
export COPTIM=${CFLAGS} |
| 296 |
export CXXOPTIM=${CXXFLAGS} |
| 297 |
# Default to -O2 if FFLAGS is unset |
| 298 |
export FC=$(tc-getFC) |
| 299 |
export FOPTIM=${FFLAGS:- -O2} |
| 300 |
export BINSORT_SCR="${T}" |
| 301 |
export CCP4_MASTER="${WORKDIR}" |
| 302 |
export CCP4I_TCLTK="${EPREFIX}/usr/bin" |
| 303 |
export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" |
| 304 |
|
| 305 |
# Can't use econf, configure rejects unknown options like --prefix |
| 306 |
./configure \ |
| 307 |
$(use_enable X x) \ |
| 308 |
--with-shared-libs \ |
| 309 |
--with-fftw="${EPREFIX}/usr" \ |
| 310 |
--with-warnings \ |
| 311 |
--disable-pdb_extract \ |
| 312 |
--disable-cctbx \ |
| 313 |
--disable-phaser \ |
| 314 |
--disable-diffractionImg \ |
| 315 |
--disable-clipper \ |
| 316 |
--disable-ssm \ |
| 317 |
--disable-mosflm \ |
| 318 |
--disable-mrbump \ |
| 319 |
--tmpdir="${TMPDIR}" \ |
| 320 |
${GENTOO_OSNAME} || die "configure failed" |
| 321 |
|
| 322 |
# We do this manually, since disabling the clipper libraries also |
| 323 |
# disables the clipper programs |
| 324 |
pushd src/clipper_progs 2>/dev/null |
| 325 |
econf \ |
| 326 |
--prefix="${S}" \ |
| 327 |
--bindir="${ED}"/usr/libexec/ccp4/bin \ |
| 328 |
--with-ccp4="${S}" \ |
| 329 |
--with-clipper="${EPREFIX}/usr" \ |
| 330 |
--with-fftw="${EPREFIX}/usr" \ |
| 331 |
--with-mmdb="${EPREFIX}/usr" \ |
| 332 |
CXX=$(tc-getCXX) |
| 333 |
popd 2>/dev/null |
| 334 |
} |
| 335 |
|
| 336 |
src_compile() { |
| 337 |
# fsplit is required for the programs |
| 338 |
pushd lib/src 2>/dev/null |
| 339 |
emake fsplit -j1 || die |
| 340 |
popd 2>/dev/null |
| 341 |
|
| 342 |
# We do this manually, since disabling the clipper libraries also |
| 343 |
# disables the clipper programs |
| 344 |
pushd src/clipper_progs 2>/dev/null |
| 345 |
emake || die |
| 346 |
popd 2>/dev/null |
| 347 |
|
| 348 |
emake -j1 || die "emake failed" |
| 349 |
} |
| 350 |
|
| 351 |
src_install() { |
| 352 |
# Set up variables for build |
| 353 |
source "${S}"/include/ccp4.setup-sh |
| 354 |
|
| 355 |
# if we don't make this, a ton of programs fail to install |
| 356 |
mkdir "${S}"/bin || die |
| 357 |
|
| 358 |
# We do this manually, since disabling the clipper libraries also |
| 359 |
# disables the clipper programs |
| 360 |
pushd "${S}"/src/clipper_progs 2>/dev/null |
| 361 |
emake install || die |
| 362 |
popd 2>/dev/null |
| 363 |
|
| 364 |
einstall || die "install failed" |
| 365 |
|
| 366 |
# Collision with sci-chemistry/mrbump |
| 367 |
rm -f "${S}"/bin/{mrbump,pydbviewer} || die |
| 368 |
|
| 369 |
# Bins |
| 370 |
exeinto /usr/libexec/ccp4/bin/ |
| 371 |
doexe "${S}"/bin/* || die |
| 372 |
|
| 373 |
# Libs |
| 374 |
for file in "${S}"/lib/*; do |
| 375 |
if [[ -d ${file} ]]; then |
| 376 |
continue |
| 377 |
elif [[ -x ${file} ]]; then |
| 378 |
dolib.so ${file} || die |
| 379 |
else |
| 380 |
insinto /usr/$(get_libdir) |
| 381 |
doins ${file} || die |
| 382 |
fi |
| 383 |
done |
| 384 |
|
| 385 |
rm -f "${S}"/include/ccp4.setup* |
| 386 |
|
| 387 |
# smartie -- log parsing |
| 388 |
insinto /usr/share/ccp4 |
| 389 |
doins -r "${S}"/share/smartie || die |
| 390 |
|
| 391 |
# Install docs and examples |
| 392 |
local _man |
| 393 |
pushd "${S}"/man/cat1 > /dev/null |
| 394 |
for _man in *; do |
| 395 |
newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} |
| 396 |
done |
| 397 |
popd > /dev/null |
| 398 |
|
| 399 |
mv "${S}"/manual/README "${S}"/manual/README-manual |
| 400 |
dodoc manual/* README CHANGES doc/* examples/README || die |
| 401 |
|
| 402 |
rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* |
| 403 |
rm "${ED}"/usr/share/doc/${PF}/COPYING.* |
| 404 |
|
| 405 |
dohtml -r "${S}"/html/* |
| 406 |
|
| 407 |
if use examples; then |
| 408 |
for i in data rnase toxd; do |
| 409 |
docinto examples/${i} |
| 410 |
dodoc "${S}"/examples/${i}/* |
| 411 |
done |
| 412 |
|
| 413 |
docinto examples/tutorial |
| 414 |
dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css |
| 415 |
for i in data results; do |
| 416 |
docinto examples/tutorial/${i} |
| 417 |
dodoc "${S}"/examples/tutorial/${i}/* |
| 418 |
done |
| 419 |
|
| 420 |
for i in non-runnable runnable; do |
| 421 |
docinto examples/unix/${i} |
| 422 |
dodoc "${S}"/examples/unix/${i}/* |
| 423 |
done |
| 424 |
fi |
| 425 |
# Needed for ccp4i docs to work |
| 426 |
dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die |
| 427 |
dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die |
| 428 |
|
| 429 |
cat >> "${T}"/baubles <<- EOF |
| 430 |
#!${EPREFIX}/bin/bash |
| 431 |
exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py |
| 432 |
EOF |
| 433 |
|
| 434 |
exeinto /usr/libexec/ccp4/bin/ |
| 435 |
doexe "${T}"/baubles || die |
| 436 |
} |
| 437 |
|
| 438 |
# Epatch wrapper for bulk patching |
| 439 |
ccp_patch() { |
| 440 |
EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
| 441 |
} |
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