Gentoo Archives: gentoo-commits

From: Justin Lecher <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-mathematics/pff/, sci-biology/minced/, sci-biology/manatee-igs/, ...
Date: Wed, 23 Sep 2015 12:48:46
Message-Id: 1443012473.6ab11cecb4abbedda99c81847ad300601de345bc.jlec@gentoo
1 commit: 6ab11cecb4abbedda99c81847ad300601de345bc
2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
3 AuthorDate: Wed Sep 23 12:47:53 2015 +0000
4 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
5 CommitDate: Wed Sep 23 12:47:53 2015 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ab11cec
7
8 Use default functions
9
10 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
11
12 sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 2 +-
13 sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild | 10 +++++-----
14 sci-biology/clview/clview-0.1.ebuild | 2 +-
15 sci-biology/consed/consed-29.ebuild | 2 +-
16 sci-biology/edena/edena-3.131028.ebuild | 2 +-
17 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 2 +-
18 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 2 +-
19 sci-biology/mgblast/mgblast-0.1.ebuild | 2 +-
20 sci-biology/minced/minced-9999.ebuild | 2 +-
21 sci-biology/pileup/pileup-0.6.ebuild | 4 ++--
22 sci-biology/pvmsx/pvmsx-0.1.ebuild | 2 +-
23 sci-biology/samstat/samstat-20130708.ebuild | 2 +-
24 sci-biology/sga/sga-9999.ebuild | 2 +-
25 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 2 +-
26 sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild | 2 +-
27 sci-chemistry/drawxtl/drawxtl-45.ebuild | 4 ++--
28 sci-chemistry/jligand/jligand-1.0.40.ebuild | 2 +-
29 sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild | 2 +-
30 sci-libs/cblas-reference/cblas-reference-20110218.ebuild | 2 +-
31 sci-libs/openlibm/openlibm-9999.ebuild | 2 +-
32 sci-libs/spglib/spglib-1.6.0.ebuild | 2 +-
33 sci-mathematics/cadabra/cadabra-1.39.ebuild | 2 +-
34 sci-mathematics/htk/htk-3.4.1.ebuild | 2 +-
35 sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild | 2 +-
36 sci-mathematics/pff/pff-8.4.ebuild | 2 +-
37 sci-mathematics/scilab/scilab-5.5.2-r1.ebuild | 2 +-
38 sci-mathematics/why3/why3-0.83.ebuild | 2 +-
39 sci-misc/foma/foma-0.9.14_alpha.ebuild | 2 +-
40 sci-misc/foma/foma-0.9.16_alpha.ebuild | 2 +-
41 sci-misc/kaldi/kaldi-0_p20150709.ebuild | 2 +-
42 sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild | 4 ++--
43 31 files changed, 38 insertions(+), 38 deletions(-)
44
45 diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
46 index 39e10af..df99ed3 100644
47 --- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
48 +++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
49 @@ -29,7 +29,7 @@ src_prepare(){
50
51 src_compile(){
52 cd src || die
53 - emake
54 + default
55 }
56
57 src_install(){
58
59 diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
60 index 47849a1..def9b35 100644
61 --- a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
62 +++ b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
63 @@ -37,19 +37,19 @@ src_configure(){
64
65 src_compile(){
66 cd jellyfish || die
67 - emake
68 + default
69
70 cd ../CA/kmer || die
71 - emake
72 + default
73
74 cd ../../CA/src || die
75 - emake
76 + default
77
78 cd ../SuperReads || die
79 - emake
80 + default
81
82 cd ../quorum || die
83 - emake
84 + default
85 }
86
87 src_install(){
88
89 diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild
90 index c8f8124..1e897bf 100644
91 --- a/sci-biology/clview/clview-0.1.ebuild
92 +++ b/sci-biology/clview/clview-0.1.ebuild
93 @@ -100,7 +100,7 @@ src_prepare() {
94
95 src_compile(){
96 cd "${S}"/clview || die
97 - emake
98 + default
99 }
100
101 src_install() {
102
103 diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
104 index 2ca1dde..b814b46 100644
105 --- a/sci-biology/consed/consed-29.ebuild
106 +++ b/sci-biology/consed/consed-29.ebuild
107 @@ -54,7 +54,7 @@ src_prepare() {
108
109 src_compile() {
110 einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
111 - emake
112 + default
113 emake -C misc/mktrace
114 emake -C misc/phd2fasta
115 (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
116
117 diff --git a/sci-biology/edena/edena-3.131028.ebuild b/sci-biology/edena/edena-3.131028.ebuild
118 index 0732977..408b875 100644
119 --- a/sci-biology/edena/edena-3.131028.ebuild
120 +++ b/sci-biology/edena/edena-3.131028.ebuild
121 @@ -26,7 +26,7 @@ src_prepare(){
122
123 src_compile(){
124 cd src
125 - emake
126 + default
127 }
128
129 src_install(){
130
131 diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
132 index 216bdcb..b30b966 100644
133 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
134 +++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
135 @@ -61,7 +61,7 @@ src_prepare(){
136 #}
137 #
138 #src_compile(){
139 -# emake
140 +# default
141 #}
142
143 src_install(){
144
145 diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
146 index 8750d19..a372621 100644
147 --- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
148 +++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
149 @@ -49,5 +49,5 @@ src_configure(){
150 }
151
152 src_compile(){
153 - emake
154 + default
155 }
156
157 diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild
158 index ff0693f..0a95c2e 100644
159 --- a/sci-biology/mgblast/mgblast-0.1.ebuild
160 +++ b/sci-biology/mgblast/mgblast-0.1.ebuild
161 @@ -37,7 +37,7 @@ src_prepare(){
162
163 src_compile(){
164 cd "${S}"/mgblast || die
165 - emake
166 + default
167 }
168
169 src_install(){
170
171 diff --git a/sci-biology/minced/minced-9999.ebuild b/sci-biology/minced/minced-9999.ebuild
172 index 8d629e1..e4aa81f 100644
173 --- a/sci-biology/minced/minced-9999.ebuild
174 +++ b/sci-biology/minced/minced-9999.ebuild
175 @@ -19,7 +19,7 @@ DEPEND=">=virtual/jdk-1.7"
176 RDEPEND=">=virtual/jre-1.7"
177
178 src_compile(){
179 - emake
180 + default
181 }
182
183 src_install(){
184
185 diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
186 index 064c48c..aaa8a56 100644
187 --- a/sci-biology/pileup/pileup-0.6.ebuild
188 +++ b/sci-biology/pileup/pileup-0.6.ebuild
189 @@ -37,12 +37,12 @@ src_prepare(){
190
191 src_compile(){
192 cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
193 - emake
194 + default
195
196 for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
197 cd "${S}"/ssaha_pileup/other_codes/$d || die "Cannot cd to "${S}"ssaha_pileup/other_codes/"$d
198 make clean
199 - emake
200 + default
201 done
202 }
203
204
205 diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
206 index f018aef..57e3b94 100644
207 --- a/sci-biology/pvmsx/pvmsx-0.1.ebuild
208 +++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild
209 @@ -35,7 +35,7 @@ src_prepare() {
210 }
211
212 src_compile() {
213 - emake
214 + default
215 }
216
217 src_install() {
218
219 diff --git a/sci-biology/samstat/samstat-20130708.ebuild b/sci-biology/samstat/samstat-20130708.ebuild
220 index 2172308..61c4135 100644
221 --- a/sci-biology/samstat/samstat-20130708.ebuild
222 +++ b/sci-biology/samstat/samstat-20130708.ebuild
223 @@ -21,7 +21,7 @@ RDEPEND="${DEPEND}"
224 S="${WORKDIR}"/"${PN}"/src
225
226 src_compile(){
227 - emake
228 + default
229 }
230
231 src_install(){
232
233 diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild
234 index 047ee21..a2d4897 100644
235 --- a/sci-biology/sga/sga-9999.ebuild
236 +++ b/sci-biology/sga/sga-9999.ebuild
237 @@ -31,7 +31,7 @@ src_configure(){
238
239 src_compile(){
240 cd src || die
241 - emake
242 + default
243 }
244
245 src_install(){
246
247 diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
248 index 3605a66..b29b5d8 100644
249 --- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
250 +++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
251 @@ -55,7 +55,7 @@ src_compile(){
252 emake OUTDIR="${WORKDIR}"/objdir out
253 emake dynamic
254 emake release
255 - emake
256 + default
257 }
258
259 src_install(){
260
261 diff --git a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild b/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
262 index 8b6445f..bac7421 100644
263 --- a/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
264 +++ b/sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild
265 @@ -68,7 +68,7 @@ src_compile() {
266
267 if use qt4; then
268 cd src/NMRdynGUI || die
269 - emake
270 + default
271 fi
272 }
273
274
275 diff --git a/sci-chemistry/drawxtl/drawxtl-45.ebuild b/sci-chemistry/drawxtl/drawxtl-45.ebuild
276 index 873394d..2585222 100644
277 --- a/sci-chemistry/drawxtl/drawxtl-45.ebuild
278 +++ b/sci-chemistry/drawxtl/drawxtl-45.ebuild
279 @@ -44,11 +44,11 @@ src_compile() {
280 mkdir exe || die "mkdir failed"
281 cd source/${MY_P} || die
282 emake clean
283 - emake
284 + default
285
286 if use fltk; then
287 cd "${S}"/source/DRAWshell${PV} || die
288 - emake
289 + default
290 fi
291 }
292
293
294 diff --git a/sci-chemistry/jligand/jligand-1.0.40.ebuild b/sci-chemistry/jligand/jligand-1.0.40.ebuild
295 index 655ca75..5d25e5b 100644
296 --- a/sci-chemistry/jligand/jligand-1.0.40.ebuild
297 +++ b/sci-chemistry/jligand/jligand-1.0.40.ebuild
298 @@ -24,7 +24,7 @@ S="${WORKDIR}"/${MY_PN}.${PV}
299
300 src_compile() {
301 sed 's:makefile::g' -i Makefile || die
302 - emake
303 + default
304 }
305
306 src_install() {
307
308 diff --git a/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild
309 index ad42bf2..9e7e1f3 100644
310 --- a/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild
311 +++ b/sci-libs/cblas-reference/cblas-reference-20110218-r1.ebuild
312 @@ -106,7 +106,7 @@ src_test() {
313 local profname=$(fortran-int64_get_profname)
314 local libname="${profname//-/_}"
315 cd testing || die
316 - emake
317 + default
318 emake run
319 }
320 multibuild_foreach_variant run_in_build_dir fortran-int64_multilib_multibuild_wrapper my_src_test
321
322 diff --git a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
323 index bd1ea4a..c2c9b6f 100644
324 --- a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
325 +++ b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
326 @@ -81,7 +81,7 @@ src_compile() {
327
328 src_test() {
329 cd testing || die
330 - emake
331 + default
332 emake run
333 }
334
335
336 diff --git a/sci-libs/openlibm/openlibm-9999.ebuild b/sci-libs/openlibm/openlibm-9999.ebuild
337 index 864627b..a088a7f 100644
338 --- a/sci-libs/openlibm/openlibm-9999.ebuild
339 +++ b/sci-libs/openlibm/openlibm-9999.ebuild
340 @@ -28,7 +28,7 @@ src_compile() {
341 }
342
343 src_test() {
344 - emake
345 + default
346 }
347
348 src_install() {
349
350 diff --git a/sci-libs/spglib/spglib-1.6.0.ebuild b/sci-libs/spglib/spglib-1.6.0.ebuild
351 index 554e394..e21553a 100644
352 --- a/sci-libs/spglib/spglib-1.6.0.ebuild
353 +++ b/sci-libs/spglib/spglib-1.6.0.ebuild
354 @@ -30,5 +30,5 @@ src_configure() {
355 }
356
357 src_compile() {
358 - emake
359 + default
360 }
361
362 diff --git a/sci-mathematics/cadabra/cadabra-1.39.ebuild b/sci-mathematics/cadabra/cadabra-1.39.ebuild
363 index ce3603b..0e19bad 100644
364 --- a/sci-mathematics/cadabra/cadabra-1.39.ebuild
365 +++ b/sci-mathematics/cadabra/cadabra-1.39.ebuild
366 @@ -51,7 +51,7 @@ src_compile() {
367
368 if use doc; then
369 cd "${S}/doc" || die
370 - emake
371 + default
372 cd doxygen/latex || die
373 emake pdf
374 fi
375
376 diff --git a/sci-mathematics/htk/htk-3.4.1.ebuild b/sci-mathematics/htk/htk-3.4.1.ebuild
377 index a073e0a..650f0ce 100644
378 --- a/sci-mathematics/htk/htk-3.4.1.ebuild
379 +++ b/sci-mathematics/htk/htk-3.4.1.ebuild
380 @@ -51,6 +51,6 @@ src_compile() {
381 if use hlmtools || use hdecode; then
382 emake -j1
383 else
384 - emake
385 + default
386 fi
387 }
388
389 diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
390 index 38b4c31..edbb9a9 100644
391 --- a/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
392 +++ b/sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild
393 @@ -21,7 +21,7 @@ src_compile() {
394 -e "s/CC=gcc/#CC=gcc/g" \
395 -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g"
396
397 - emake
398 + default
399 }
400
401 src_install() {
402
403 diff --git a/sci-mathematics/pff/pff-8.4.ebuild b/sci-mathematics/pff/pff-8.4.ebuild
404 index 2c221ad..d6c235a 100644
405 --- a/sci-mathematics/pff/pff-8.4.ebuild
406 +++ b/sci-mathematics/pff/pff-8.4.ebuild
407 @@ -25,7 +25,7 @@ src_prepare() {
408 }
409
410 src_compile(){
411 - emake
412 + default
413 }
414
415 src_install(){
416
417 diff --git a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
418 index 432ffdd..fabaeb0 100644
419 --- a/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
420 +++ b/sci-mathematics/scilab/scilab-5.5.2-r1.ebuild
421 @@ -232,7 +232,7 @@ src_configure() {
422
423 src_compile() {
424 addpredict /proc/mtrr
425 - emake
426 + default
427 pax-mark m .libs/scilab-bin
428 use doc && emake doc
429 }
430
431 diff --git a/sci-mathematics/why3/why3-0.83.ebuild b/sci-mathematics/why3/why3-0.83.ebuild
432 index 7ff2827..b07bcc3 100644
433 --- a/sci-mathematics/why3/why3-0.83.ebuild
434 +++ b/sci-mathematics/why3/why3-0.83.ebuild
435 @@ -40,7 +40,7 @@ src_configure() {
436 src_compile() {
437 MAKEOPTS+=" -j1"
438
439 - emake
440 + default
441 if use doc; then
442 emake doc/manual.pdf
443 fi
444
445 diff --git a/sci-misc/foma/foma-0.9.14_alpha.ebuild b/sci-misc/foma/foma-0.9.14_alpha.ebuild
446 index 20ef0c6..52fca31 100644
447 --- a/sci-misc/foma/foma-0.9.14_alpha.ebuild
448 +++ b/sci-misc/foma/foma-0.9.14_alpha.ebuild
449 @@ -33,7 +33,7 @@ src_prepare() {
450 }
451
452 src_compile() {
453 - emake
454 + default
455 emake libfoma
456 }
457
458
459 diff --git a/sci-misc/foma/foma-0.9.16_alpha.ebuild b/sci-misc/foma/foma-0.9.16_alpha.ebuild
460 index 0607dc0..37700c3 100644
461 --- a/sci-misc/foma/foma-0.9.16_alpha.ebuild
462 +++ b/sci-misc/foma/foma-0.9.16_alpha.ebuild
463 @@ -33,7 +33,7 @@ src_prepare() {
464 }
465
466 src_compile() {
467 - emake
468 + default
469 emake libfoma
470 }
471
472
473 diff --git a/sci-misc/kaldi/kaldi-0_p20150709.ebuild b/sci-misc/kaldi/kaldi-0_p20150709.ebuild
474 index 0ce2b8a..ad8c84d 100644
475 --- a/sci-misc/kaldi/kaldi-0_p20150709.ebuild
476 +++ b/sci-misc/kaldi/kaldi-0_p20150709.ebuild
477 @@ -47,7 +47,7 @@ src_configure() {
478 }
479
480 src_compile() {
481 - emake
482 + default
483 use doc && doxygen
484 }
485
486
487 diff --git a/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild b/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
488 index f79c02c..c00fbca 100644
489 --- a/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
490 +++ b/sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild
491 @@ -34,7 +34,7 @@ src_compile() {
492 source $(ls -1 "${EROOT}"usr/share/Geant4-*/geant4make/geant4make.sh) || die
493 for d in ${dirs}; do
494 pushd ${d} > /dev/null || die
495 - emake
496 + default
497 if use doc; then
498 doxygen || die
499 fi
500 @@ -44,7 +44,7 @@ src_compile() {
501
502 src_test() {
503 cd examples || die
504 - emake
505 + default
506 ./run_suite.sh || die
507 }