1 |
jlec 10/12/31 12:24:48 |
2 |
|
3 |
Modified: ChangeLog |
4 |
Added: ccp4-libs-6.1.3-r5.ebuild |
5 |
Log: |
6 |
Install missing file like enviro.def |
7 |
|
8 |
(Portage version: 2.2.0_alpha10/cvs/Linux x86_64) |
9 |
|
10 |
Revision Changes Path |
11 |
1.18 sci-libs/ccp4-libs/ChangeLog |
12 |
|
13 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.18&view=markup |
14 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.18&content-type=text/plain |
15 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.17&r2=1.18 |
16 |
|
17 |
Index: ChangeLog |
18 |
=================================================================== |
19 |
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v |
20 |
retrieving revision 1.17 |
21 |
retrieving revision 1.18 |
22 |
diff -u -r1.17 -r1.18 |
23 |
--- ChangeLog 20 Dec 2010 12:28:01 -0000 1.17 |
24 |
+++ ChangeLog 31 Dec 2010 12:24:48 -0000 1.18 |
25 |
@@ -1,6 +1,11 @@ |
26 |
# ChangeLog for sci-libs/ccp4-libs |
27 |
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 |
28 |
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.17 2010/12/20 12:28:01 hwoarang Exp $ |
29 |
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.18 2010/12/31 12:24:48 jlec Exp $ |
30 |
+ |
31 |
+*ccp4-libs-6.1.3-r5 (31 Dec 2010) |
32 |
+ |
33 |
+ 31 Dec 2010; <justin@g.o> +ccp4-libs-6.1.3-r5.ebuild: |
34 |
+ Install missing file like enviro.def |
35 |
|
36 |
20 Dec 2010; Markos Chandras <hwoarang@g.o> ccp4-libs-6.1.3-r4.ebuild: |
37 |
Stable on amd64 wrt bug #348872 |
38 |
|
39 |
|
40 |
|
41 |
1.1 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild |
42 |
|
43 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild?rev=1.1&view=markup |
44 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild?rev=1.1&content-type=text/plain |
45 |
|
46 |
Index: ccp4-libs-6.1.3-r5.ebuild |
47 |
=================================================================== |
48 |
# Copyright 1999-2010 Gentoo Foundation |
49 |
# Distributed under the terms of the GNU General Public License v2 |
50 |
# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r5.ebuild,v 1.1 2010/12/31 12:24:48 jlec Exp $ |
51 |
|
52 |
EAPI="3" |
53 |
|
54 |
inherit eutils gnuconfig multilib toolchain-funcs |
55 |
|
56 |
SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
57 |
|
58 |
#UPDATE="04_03_09" |
59 |
#PATCHDATE="090511" |
60 |
|
61 |
MY_P="${P/-libs}" |
62 |
|
63 |
PATCH_TOT="0" |
64 |
# Here's a little scriptlet to generate this list from the provided |
65 |
# index.patches file |
66 |
# |
67 |
# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; |
68 |
# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < |
69 |
# index.patches |
70 |
#PATCH1=( src/topp_ |
71 |
#topp.f-r1.16.2.5-r1.16.2.6.diff ) |
72 |
#PATCH2=( . |
73 |
#configure-r1.372.2.18-r1.372.2.19.diff ) |
74 |
|
75 |
DESCRIPTION="Protein X-ray crystallography toolkit" |
76 |
HOMEPAGE="http://www.ccp4.ac.uk/" |
77 |
SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" |
78 |
# patch tarball from upstream |
79 |
[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
80 |
# patches created by us |
81 |
[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
82 |
|
83 |
for i in $(seq $PATCH_TOT); do |
84 |
NAME="PATCH${i}[1]" |
85 |
SRC_URI="${SRC_URI} |
86 |
${SRC}/${PV}/patches/${!NAME}" |
87 |
done |
88 |
|
89 |
LICENSE="ccp4" |
90 |
SLOT="0" |
91 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
92 |
IUSE="" |
93 |
|
94 |
RDEPEND=" |
95 |
virtual/jpeg |
96 |
app-shells/tcsh |
97 |
!<sci-chemistry/ccp4-6.1.3 |
98 |
!<sci-chemistry/ccp4-apps-6.1.3-r6 |
99 |
sci-libs/cbflib |
100 |
=sci-libs/fftw-2* |
101 |
sci-libs/mmdb |
102 |
sci-libs/monomer-db |
103 |
virtual/lapack |
104 |
virtual/blas" |
105 |
DEPEND="${RDEPEND}" |
106 |
|
107 |
S="${WORKDIR}/${MY_P}" |
108 |
|
109 |
src_prepare() { |
110 |
einfo "Applying upstream patches ..." |
111 |
for patch in $(seq $PATCH_TOT); do |
112 |
base="PATCH${patch}" |
113 |
dir=$(eval echo \${${base}[0]}) |
114 |
p=$(eval echo \${${base}[1]}) |
115 |
pushd "${dir}" >& /dev/null |
116 |
ccp_patch "${DISTDIR}/${p}" |
117 |
popd >& /dev/null |
118 |
done |
119 |
einfo "Done." |
120 |
echo |
121 |
|
122 |
[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
123 |
|
124 |
einfo "Applying Gentoo patches ..." |
125 |
# fix buffer overflows wrt bug 339706 |
126 |
ccp_patch "${FILESDIR}"/${PV}-overflows.patch |
127 |
|
128 |
# it tries to create libdir, bindir etc on live system in configure |
129 |
ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
130 |
|
131 |
# gerror_ gets defined twice on ppc if you're using gfortran/g95 |
132 |
ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch |
133 |
|
134 |
# make creation of libccif.so smooth |
135 |
ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch |
136 |
|
137 |
# lets try to build libmmdb seperatly |
138 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch |
139 |
|
140 |
# unbundle libjpeg and cbflib |
141 |
ccp_patch "${FILESDIR}"/${PV}-unbundle-libs.patch |
142 |
|
143 |
# Fix missing DESTIDR |
144 |
# not installing during build |
145 |
ccp_patch "${FILESDIR}"/${PV}-noinstall.patch |
146 |
sed \ |
147 |
-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ |
148 |
-i configure || die |
149 |
|
150 |
einfo "Done." # done applying Gentoo patches |
151 |
echo |
152 |
|
153 |
sed \ |
154 |
-e "s:/usr:${EPREFIX}/usr:g" \ |
155 |
-e 's:-Wl,-rpath,$CLIB::g' \ |
156 |
-e 's: -rpath $CLIB::g' \ |
157 |
-e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
158 |
-i configure || die |
159 |
|
160 |
gnuconfig_update |
161 |
} |
162 |
|
163 |
src_configure() { |
164 |
|
165 |
rm -rf lib/DiffractionImage/{jpg,CBFlib} || die |
166 |
|
167 |
# Build system is broken if we set LDFLAGS |
168 |
userldflags="${LDFLAGS}" |
169 |
export SHARED_LIB_FLAGS="${LDFLAGS}" |
170 |
unset LDFLAGS |
171 |
|
172 |
# GENTOO_OSNAME can be one of: |
173 |
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
174 |
# linux_compaq_compilers linux_intel_compilers generic Darwin |
175 |
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
176 |
if [[ "$(tc-getFC)" = "ifort" ]]; then |
177 |
if use ia64; then |
178 |
GENTOO_OSNAME="ia64_linux_intel" |
179 |
else |
180 |
# Should be valid for x86, maybe amd64 |
181 |
GENTOO_OSNAME="linux_intel_compilers" |
182 |
fi |
183 |
else |
184 |
# Should be valid for x86 and amd64, at least |
185 |
GENTOO_OSNAME="linux" |
186 |
fi |
187 |
|
188 |
# Sets up env |
189 |
ln -s \ |
190 |
ccp4.setup-bash \ |
191 |
"${S}"/include/ccp4.setup |
192 |
|
193 |
# We agree to the license by emerging this, set in LICENSE |
194 |
sed -i \ |
195 |
-e "s~^\(^agreed=\).*~\1yes~g" \ |
196 |
"${S}"/configure |
197 |
|
198 |
# Fix up variables -- need to reset CCP4_MASTER at install-time |
199 |
sed -i \ |
200 |
-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \ |
201 |
-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
202 |
"${S}"/include/ccp4.setup* |
203 |
|
204 |
# Set up variables for build |
205 |
source "${S}"/include/ccp4.setup |
206 |
|
207 |
export CC=$(tc-getCC) |
208 |
export CXX=$(tc-getCXX) |
209 |
export COPTIM=${CFLAGS} |
210 |
export CXXOPTIM=${CXXFLAGS} |
211 |
# Default to -O2 if FFLAGS is unset |
212 |
export FC=$(tc-getFC) |
213 |
export FOPTIM=${FFLAGS:- -O2} |
214 |
# export CCP4_SCR="${T}" |
215 |
|
216 |
# Fix linking |
217 |
# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \ |
218 |
export SHARE_LIB="\ |
219 |
$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ |
220 |
$(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" |
221 |
|
222 |
# Can't use econf, configure rejects unknown options like --prefix |
223 |
./configure \ |
224 |
--onlylibs \ |
225 |
--with-shared-libs \ |
226 |
--with-fftw="${EPREFIX}"/usr \ |
227 |
--with-warnings \ |
228 |
--disable-cctbx \ |
229 |
--disable-clipper \ |
230 |
--tmpdir="${TMPDIR}" \ |
231 |
--bindir="${EPREFIX}"/usr/libexec/ccp4/bin/ \ |
232 |
--libdir="${EPREFIX}"/usr/$(get_libdir) \ |
233 |
${GENTOO_OSNAME} || die "econf failed" |
234 |
} |
235 |
|
236 |
src_compile() { |
237 |
emake -j1 \ |
238 |
DESTDIR="${D}" onlylib || die "emake failed" |
239 |
} |
240 |
|
241 |
src_install() { |
242 |
# Set up variables for build |
243 |
source "${S}"/include/ccp4.setup |
244 |
|
245 |
emake -j1 \ |
246 |
DESTDIR="${D}" \ |
247 |
includedir="${EPREFIX}"/usr/include \ |
248 |
library_includedir="${EPREFIX}"/usr/include \ |
249 |
install || die |
250 |
|
251 |
# Libs |
252 |
for file in "${S}"/lib/*; do |
253 |
if [[ -d ${file} ]]; then |
254 |
continue |
255 |
elif [[ -x ${file} ]]; then |
256 |
dolib.so ${file} || die |
257 |
else |
258 |
insinto /usr/$(get_libdir) |
259 |
doins ${file} || die |
260 |
fi |
261 |
done |
262 |
|
263 |
# Fix libdir in all *.la files |
264 |
sed -i \ |
265 |
-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \ |
266 |
"${ED}"/usr/$(get_libdir)/*.la || die |
267 |
|
268 |
# Data |
269 |
insinto /usr/share/ccp4/data/ |
270 |
doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die |
271 |
|
272 |
# Environment files, setup scripts, etc. |
273 |
rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die |
274 |
insinto /usr/share/ccp4/ |
275 |
doins -r "${S}"/include || die |
276 |
|
277 |
dodoc "${S}"/lib/data/*.doc || die |
278 |
newdoc "${S}"/lib/data/README DATA-README || die |
279 |
} |
280 |
|
281 |
# Epatch wrapper for bulk patching |
282 |
ccp_patch() { |
283 |
EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
284 |
} |