Gentoo Archives: gentoo-commits

From: Benda XU <heroxbd@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/selfdeps.d/, config/simple-deprules.d/, ...
Date: Wed, 30 May 2018 05:31:43
Message-Id: 1527657920.3f7c507a97b62ef814517adf3e9fae935db4ad04.heroxbd@gentoo
1 commit: 3f7c507a97b62ef814517adf3e9fae935db4ad04
2 Author: Benda Xu <heroxbd <AT> gentoo <DOT> org>
3 AuthorDate: Wed May 30 05:25:20 2018 +0000
4 Commit: Benda XU <heroxbd <AT> gentoo <DOT> org>
5 CommitDate: Wed May 30 05:25:20 2018 +0000
6 URL: https://gitweb.gentoo.org/proj/R_overlay.git/commit/?id=3f7c507a
7
8 Use regex in dep string matches.
9
10 Ignore rules should come later than positive rules.
11
12 Closes: https://bugs.gentoo.org/653694
13
14 config/simple-deprules.d/R | 66 ++++++------
15 config/simple-deprules.d/app | 7 +-
16 config/simple-deprules.d/app-text | 29 +-----
17 config/simple-deprules.d/compound_deps | 25 ++---
18 config/simple-deprules.d/dev | 58 ++---------
19 config/simple-deprules.d/dev-libs | 73 +++-----------
20 config/simple-deprules.d/dot_remap | 134 -------------------------
21 config/simple-deprules.d/ignored_text | 103 ++++++-------------
22 config/simple-deprules.d/media | 20 +---
23 config/simple-deprules.d/media-libs | 30 ++----
24 config/simple-deprules.d/misc | 6 +-
25 config/simple-deprules.d/net | 21 +---
26 config/simple-deprules.d/nvidia | 22 ++--
27 config/simple-deprules.d/sci | 34 +++----
28 config/simple-deprules.d/sci-libs | 35 ++-----
29 config/simple-deprules.d/selfdeps | 22 ----
30 config/simple-deprules.d/selfdeps.d/sci-CRAN | 23 ++---
31 config/simple-deprules.d/sys | 32 +++---
32 config/simple-deprules.d/system.set | 39 ++-----
33 config/simple-deprules.d/unknown | 5 +-
34 config/simple-deprules.d/x11 | 12 +--
35 roverlay/depres/simpledeprule/abstractrules.py | 10 +-
36 roverlay/depres/simpledeprule/rules.py | 6 +-
37 23 files changed, 195 insertions(+), 617 deletions(-)
38
39 diff --git a/config/simple-deprules.d/R b/config/simple-deprules.d/R
40 index 9106deb..8edf111 100644
41 --- a/config/simple-deprules.d/R
42 +++ b/config/simple-deprules.d/R
43 @@ -6,53 +6,43 @@
44 #deptype all
45
46 # using fuzzy dep matches
47 -~dev-lang/R :: R
48 +~dev-lang/R :: ^R$
49
50 dev-lang/R[tk] {
51 - tcl/tk 8.5
52 - Tcl/Tk (>= 8.5)
53 - tcltk (but only for the GUI
54 -}
55 -
56 -# base packages that always assumed to be provided by dev-lang/R (taken from generate_ebuild)
57 -% {
58 - base
59 - compiler
60 - datasets
61 - graphics
62 - grDevices
63 - grid
64 - methods
65 - parallel
66 - splines
67 - stats
68 - stats4
69 + tcl/tk
70 tcltk
71 - tools
72 - utils
73 }
74
75 -# FIXME, seems to be provided too
76 -% {
77 - stepfun
78 - ts
79 - package ts
80 - package ts (included in the R release)
81 -}
82 # modreg is in stats, according to https://stat.ethz.ch/pipermail/bioconductor/2010-June/034197.html
83 ! :: modreg
84
85 # R is always compiled with '--enabled-R-shlib'
86 ! {
87 - R must be compiled with --enable-R-shlib if the server is to be built
88 - R must be compiled with --enable-R-shlib if theserver is to be built
89 - R must be compiled with --enable-R-shlibif the server is to be built
90 - Download regular shlib (420 KB) from externalsource ('xls.getshlib()' or manually)
91 - R built as a shared object
92 - R built as a shared object.
93 - R built as a shared or static (R >= 2.7.0) library
94 - R built as a shared orstatic library
95 + --enable-R-shlib
96 + xls.getshlib
97 + R built as a shared
98 R-0.64 or later
99 - Regular shlib must be obtained from an externalsource (use 'xls.getshlib()' or dl manually).
100 - dl regular shlib with 'xls.getshlib()'or manually (~420 KB)
101 +}
102 +
103 +# base packages that always assumed to be provided by dev-lang/R (taken from generate_ebuild)
104 +% {
105 + ^base$
106 + ^compiler$
107 + ^datasets$
108 + ^graphics$
109 + ^grDevices$
110 + ^grid$
111 + ^methods$
112 + ^parallel$
113 + ^splines$
114 + ^stats4?
115 + ^tools$
116 + ^utils$
117 +}
118 +
119 +# FIXME, seems to be provided too
120 +% {
121 + ^stepfun$
122 + ^ts$
123 + package.*ts
124 }
125
126 diff --git a/config/simple-deprules.d/app b/config/simple-deprules.d/app
127 index 99ba3c3..6c086c4 100644
128 --- a/config/simple-deprules.d/app
129 +++ b/config/simple-deprules.d/app
130 @@ -3,10 +3,7 @@
131 app-admin/ec2-api-tools :: ec2-api-tools
132
133 # FIXME zip or unzip?
134 -app-arch/zip :: zip
135 +app-arch/zip :: ^zip$
136
137 # FIXME: this is not satisfiable, latest dieharder version in portage is 2.28.1
138 -app-crypt/dieharder {
139 - DieHarder library (>= 2.8.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php
140 - DieHarder library (>= 3.31.1) fromhttp://www.phy.duke.edu/~rgb/General/dieharder.php
141 -}
142 +app-crypt/dieharder :: DieHarder
143 \ No newline at end of file
144
145 diff --git a/config/simple-deprules.d/app-text b/config/simple-deprules.d/app-text
146 index 6e4cdd4..810178c 100644
147 --- a/config/simple-deprules.d/app-text
148 +++ b/config/simple-deprules.d/app-text
149 @@ -1,35 +1,16 @@
150 #deptype sys
151
152 -app-text/antiword {
153 - Antiword (http://www.winfield.demon.nl/) forreading MS Word files
154 - antiword for reading MS Word files
155 - Antiword (<http://www.winfield.demon.nl/>) forreading MS Word files
156 -}
157 +app-text/antiword :: Antiword
158
159 ~app-text/ghostscript-gpl :: ghostscript
160
161 app-text/poppler {
162 - pdfinfo andpdftotext for reading PDF
163 - pdfinfo and pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF
164 - pdftotext from Poppler(http://poppler.freedesktop.org/) for reading PDF
165 -}
166 -
167 -# pdflatex?
168 -app-text/texlive {
169 - (PDF)LaTeX (http://www.latex-project.org/) withpdfpages package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs.
170 - (PDF)LaTeX (http://www.latex-project.org/) with'pdfpages' package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs.
171 - (PDF)LaTeX for saveLatex()
172 -}
173 -
174 -app-text/poppler {
175 + poppler
176 pdfinfo
177 + pdftotext
178 }
179
180 +# pdflatex?
181 +app-text/texlive :: LaTeX
182
183 ~app-text/pandoc :: pandoc
184 -app-text/pandoc {
185 - pandoc (>= 1.12.3) -http://johnmacfarlane.net/pandoc
186 - pandoc with https support
187 - Package vignettes based on R Markdown v2 requirePandoc (http://pandoc.org). The function rst2pdf() andvignettes based on reStructuredText require rst2pdf(https://github.com/rst2pdf/rst2pdf).
188 -}
189 -
190
191 diff --git a/config/simple-deprules.d/compound_deps b/config/simple-deprules.d/compound_deps
192 index 963ee0f..b0c0133 100644
193 --- a/config/simple-deprules.d/compound_deps
194 +++ b/config/simple-deprules.d/compound_deps
195 @@ -2,50 +2,45 @@
196
197 ( media-libs/fontconfig media-fonts/corefonts ) {
198 fontconfig and msttcorefonts
199 - fontconfig and msttcorefonts recommended)
200 }
201
202 ( net-libs/liboauth net-misc/curl ) {
203 - liboauth (>= 0.9.4) liboauth.sourceforge.net andlibcurl http://curl.haxx.se
204 + liboauth.*curl
205 }
206
207 # FIXME
208 ( sci-libs/blas-atlas dev-util/nvidia-cuda-toolkit ) {
209 - Atlas development build as well as a Nvidia GPU withCUDA support
210 + Atlas.*Nvidia GPU.*CUDA
211 }
212
213 || ( dev-libs/libxml2 dev-libs/expat ) {
214 - Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml)
215 - Daniel Veillard's libxml(ftp://ftp.gnome.org/pub/GNOME/stable/sources/libxml/)and/orJim Clark's expat (http://www.jclark.com/xml)
216 + libxml.*expat
217 }
218
219 ( media-libs/tiff >=sci-libs/fftw-3 ) {
220 - optional libtiff and fftw3
221 + libtiff.*fftw3
222 }
223
224 ( sci-libs/gdal sci-libs/proj ) {
225 - for building from source: GDAL >= 1.3.1 && GDAL < 1.6.0 (until tested) library and PROJ.4 (proj >= 4.4.9)
226 - for building from source: GDAL >= 1.3.1 library and PROJ.4 (proj >= 4.4.9)
227 - for building from source: GDAL >= 1.3.1 library and PROJ.4(proj >= 4.4.9)
228 - for building from source: GDAL >= 1.6.0 library and PROJ.4(proj >= 4.4.9)
229 + GDAL.*PROJ.4
230 }
231
232 ( dev-libs/mpfr dev-libs/gmp ) {
233 - http://mpfr.org/) and GMP (GNU Multiple Precision library
234 + mpfr.*GMP
235 }
236
237 || ( media-gfx/imagemagick media-gfx/graphicsmagick ) {
238 - ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) for saveGIF()
239 + ImageMagick.*GraphicsMagick
240 }
241
242 || ( media-gfx/imagemagick media-gfx/graphicsmagick app-office/lyx ) {
243 - ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) or LyX(http://www.lyx.org) for saveGIF()
244 + ImageMagick.*GraphicsMagick.*LyX
245 }
246
247 || ( media-libs/tiff virtual/jpeg ) {
248 - libtiff and/or libjpeg
249 + libtiff.*libjpeg
250 }
251
252 ( virtual/blas virtual/lapack ) {
253 - BLAS/LAPACK libraries
254 + BLAS.*LAPACK
255 }
256
257 diff --git a/config/simple-deprules.d/dev b/config/simple-deprules.d/dev
258 index 89759fc..faa01d9 100644
259 --- a/config/simple-deprules.d/dev
260 +++ b/config/simple-deprules.d/dev
261 @@ -10,74 +10,34 @@ dev-cpp/gtkmm :: gtkmm-2.4
262 }
263
264 # FIXME
265 -dev-db/unixODBC {
266 - An ODBC driver manager and drivers. See README.
267 - An ODBC3 driver manager and drivers.
268 - An ODBC3 driver manager and drivers. See README.
269 - ODBC support and a back end database
270 -}
271 +dev-db/unixODBC :: ODBC
272
273 -dev-java/ant :: ant
274 +dev-java/ant :: ^ant$
275 dev-java/jdbc-postgresql :: PostgreSQL JDBCdriver
276
277 -
278 -# try to slot-match dev-lang/python, but use known slots only
279 -~dev-lang/python:slotparts=2:restrict=2.7,3.2,3.3,3.4 {
280 - python
281 - python headers
282 -}
283 # else fall back to fuzzy
284 ~dev-lang/python {
285 - python
286 + ^python
287 }
288 # lowest python version in portage: 2.7 (2.6 masked)
289 dev-lang/python {
290 - Python (>= 2.4) to run Asciidoc(http://www.python.org/)
291 - Python 2.7.x or Python 3.2.x-3.4.x
292 + ^Python
293 }
294
295 -
296 dev-lang/lua :: lua version>= 5.1.4
297 ~dev-lang/lua :: lua
298
299 -~dev-tex/pgf {
300 - pgf
301 -}
302 +~dev-tex/pgf :: ^pgf$
303
304 ->=dev-tex/pgf-2.10 {
305 - pgf (>=2.10) (http://sourceforge.net/projects/pgf/)for the vignette
306 -}
307 +>=dev-tex/pgf-2.10 :: pgf.*>=2.10
308
309 -~dev-tcltk/bwidget {
310 - bwidget
311 - Tcl/Tk extensions BWidget
312 -}
313 +~dev-tcltk/bwidget :: bwidget
314
315 ~dev-tcltk/tktable :: tktable
316
317 -dev-util/cmake {
318 - cmake
319 - cmake (http://www.cmake.org)
320 -}
321 -
322 -~dev-python/numpy {
323 - numpy
324 -}
325 +dev-util/cmake :: cmake
326
327 -# FIXME: the jdk rules are not quite correct,
328 -# virtual/jdk:1.7 (probably) works for some packages, too
329 -#
330 -~virtual/jdk:slotparts=i1.6:restrict=1.6,6.0 {
331 - java
332 - Java version
333 - java runtime
334 -}
335 -
336 -~virtual/jdk:slotparts=i1.7:restrict=1.7,7.0 {
337 - java
338 - Java version
339 - java runtime
340 -}
341 +~dev-python/numpy :: numpy
342
343 # slot-relative rules take precedence
344 # TODO: slot-restricted rules should get a lower priority
345
346 diff --git a/config/simple-deprules.d/dev-libs b/config/simple-deprules.d/dev-libs
347 index b46d2a6..b0faa08 100644
348 --- a/config/simple-deprules.d/dev-libs
349 +++ b/config/simple-deprules.d/dev-libs
350 @@ -1,95 +1,52 @@
351 #deptype sys
352
353 -~dev-libs/atk :: ATK
354 +~dev-libs/atk :: ^ATK$
355
356 ~dev-libs/openssl :: OpenSSL
357
358 -~dev-libs/boost {
359 - boost library
360 - boost
361 -}
362 -dev-libs/boost {
363 - Boost C++ libraries (1.31 or greater)
364 - Boost library (>= 1.34.0) from http://www.boost.org
365 - Boost library (>= 1.34.0) fromhttp://www.boost.org
366 - Boost library from http://www.boost.org
367 - Boost libraryfrom http://www.boost.org
368 - boost headers for smart pointers
369 - The Boost 'program_options' library(http://boost.org) is required.
370 - Boost (or the BoostHeaders package)
371 -}
372 +~dev-libs/boost :: boost
373
374 -~dev-libs/glib {
375 - glib
376 - glib2
377 -}
378 +~dev-libs/glib :: glib
379
380 ~dev-libs/gmp {
381 libgmp
382 - gmp
383 -}
384 -~dev-libs/gmp {
385 - GMP (GNU MP bignum library
386 - GMP (GNU MP bignum library)
387 - GMP (GNU Multiple Precision library
388 - http://gmplib.org/)
389 + ^gmp
390 + gmplib
391 }
392
393 ~dev-libs/libffi :: libffi
394
395 ~dev-libs/libpcre {
396 - libpcre
397 pcre
398 }
399
400 ~dev-libs/libxml2 {
401 - xml
402 - xml2
403 - libxml
404 - libxml2
405 + ^xml
406 + ^libxml
407 }
408
409 ~dev-libs/libxslt :: libxslt
410
411 dev-libs/mpc {
412 - and MPC (Multiple Precision ComplexLibrary
413 - http://www.multiprecision.org/)
414 + ^mpc$
415 + multi.*precision
416 }
417
418 -~dev-libs/mpfr {
419 - MPFR (MP Floating-Point Reliable Library
420 - mpfr
421 - http://mpfr.org/)
422 -}
423 +~dev-libs/mpfr :: mpfr
424 +
425 # FIXME versions -> fuzzy
426 -dev-libs/quantlib {
427 - QuantLib libraries must be installed
428 - QuantLib library (>= 0.8.1) from http://quantlib.org
429 - QuantLib library (>= 0.9.0) from http://quantlib.org
430 - QuantLib library (>= 0.9.7) from http://quantlib.org
431 - QuantLib library (>= 0.9.7) fromhttp://quantlib.org
432 - QuantLib library (>= 0.9.9) fromhttp://quantlib.org
433 - QuantLib library from http://quantlib.org
434 -}
435 +dev-libs/quantlib :: QuantLib
436
437 ~dev-libs/quantlib {
438 QuantLib library
439 }
440
441 -~dev-libs/xerces-c {
442 - xerces-c
443 - libxerces-c
444 -}
445 +~dev-libs/xerces-c :: xerces-c
446
447 ~sys-devel/clang {
448 clang
449 }
450
451 -dev-libs/geoip {
452 - GeoIP from MaxMinds
453 -}
454 +dev-libs/geoip :: GeoIP
455
456 -dev-libs/icu {
457 - ICU4C (>= 50
458 - ICU4C (>= 52
459 -}
460 +dev-libs/icu :: ICU4C
461
462 diff --git a/config/simple-deprules.d/dot_remap b/config/simple-deprules.d/dot_remap
463 deleted file mode 100644
464 index 03aa2f4..0000000
465 --- a/config/simple-deprules.d/dot_remap
466 +++ /dev/null
467 @@ -1,134 +0,0 @@
468 -#! NOPARSE
469 -#
470 -# !!! This file should no longer be necessary
471 -# (the dynamic selfdep pool is able to remap dots automatically)
472 -#
473 -
474 -#deptype pkg,selfdep
475 -
476 -~sci-R/aroma_affymetrix :: aroma.affymetrix
477 -~sci-R/aroma_apd :: aroma.apd
478 -~sci-R/aroma_core :: aroma.core
479 -~sci-R/aroma_light :: aroma.light
480 -
481 -~sci-R/bio_infer :: bio.infer
482 -
483 -~sci-R/Ckmeans_1d_dp :: Ckmeans.1d.dp
484 -~sci-R/clim_pact :: clim.pact
485 -~sci-R/compute_es :: compute.es
486 -~sci-R/conf_design :: conf.design
487 -
488 -~sci-R/data_table :: data.table
489 -~sci-R/DoE_base :: DoE.base
490 -~sci-R/DoE_wrapper :: DoE.wrapper
491 -
492 -~sci-R/ergm_userterms :: ergm.userterms
493 -
494 -~sci-R/FrF2_catlg128 :: FrF2.catlg128
495 -~sci-R/FunciSNP :: FunciSNP.data
496 -~sci-R/futile_any :: futile.any
497 -~sci-R/futile_logger :: futile.logger
498 -~sci-R/futile_matrix :: futile.matrix
499 -~sci-R/futile_options :: futile.options
500 -~sci-R/futile_paradigm :: futile.paradigm
501 -
502 -~sci-R/gamlss_data :: gamlss.data
503 -~sci-R/gamlss_dist :: gamlss.dist
504 -~sci-R/gamlss_nl :: gamlss.nl
505 -~sci-R/gamlss_tr :: gamlss.tr
506 -~sci-R/gamlss_util :: gamlss.util
507 -~sci-R/GO_db :: GO.db
508 -
509 -~sci-R/haplo_score :: haplo_score
510 -~sci-R/haplo_stats :: haplo_stats
511 -~sci-R/heapmap_plus :: heatmap.plus
512 -
513 -~sci-R/lava_tobit :: lava.tobit
514 -
515 -~sci-R/minpack_lm :: minpack.lm
516 -
517 -~sci-R/opencpu_encode :: opencpu.encode
518 -~sci-R/openNLPmodels_en :: openNLPmodels.en
519 -~sci-R/openNLPmodels_es :: openNLPmodels.es
520 -~sci-R/operator_tools :: operator.tools
521 -~sci-R/orloca_es :: orloca.es
522 -~sci-R/oro_dicom :: oro.dicom
523 -~sci-R/oro_nifti :: oro.nifti
524 -
525 -~sci-R/org_Ag_eg_db :: org.Ag.eg.db
526 -~sci-R/org_At_tair_db :: org.At.tair.db
527 -~sci-R/org_Bt_eg_db :: org.Bt.eg.db
528 -~sci-R/org_Ce_eg_db :: org.Ce.eg.db
529 -~sci-R/org_Cf_eg_db :: org.Cf.eg.db
530 -~sci-R/org_Dm_eg_db :: org.Dm.eg.db
531 -~sci-R/org_Dr_eg_db :: org.Dr.eg.db
532 -~sci-R/org_EcK12_eg_db :: org.EcK12.eg.db
533 -~sci-R/org_EcSakai_eg_db :: org.EcSakai.eg.db
534 -~sci-R/org_Gg_eg_db :: org.Gg.eg.db
535 -~sci-R/org_Hs_eg_db :: org.Hs.eg.db
536 -~sci-R/org_Mm_eg_db :: org.Mm.eg.db
537 -~sci-R/org_Mmu_eg_db :: org.Mmu.eg.db
538 -~sci-R/org_Pf_plasmo_db :: org.Pf.plasmo.db
539 -~sci-R/org_Pt_eg_db :: org.Pt.eg.db
540 -~sci-R/org_Rn_eg_db :: org.Rn.eg.db
541 -~sci-R/org_Sc_sgd_db :: org.Sc.sgd.db
542 -~sci-R/org_Sco_eg_db :: org.Sco.eg.db
543 -~sci-R/org_Ss_eg_db :: org.Ss.eg.db
544 -~sci-R/org_Xl_eg_db :: org.Xl.eg.db
545 -
546 -~sci-R/R_cache :: R.cache
547 -~sci-R/RcmdrPlugin_IPSUR :: RcmdrPlugin.IPSUR
548 -~sci-R/R_devices :: R.devices
549 -~sci-R/R_filesets :: R.filesets
550 -~sci-R/R_huge :: R.huge
551 -~sci-R/R_matlab :: R.matlab
552 -~sci-R/R_methodsS3 :: R.methodsS3
553 -~sci-R/ROI_plugin_glpk :: ROI.plugin.glpk
554 -~sci-R/ROI_plugin_quadprog :: ROI.plugin.quadprog
555 -~sci-R/ROI_plugin_symphony :: ROI.plugin.symphony
556 -~sci-R/R_oo :: R.oo
557 -~sci-R/rpart_plot :: rpart.plot
558 -~sci-R/R_rsp :: R.rsp
559 -~sci-R/RSQLite_extfuns :: RSQLite.extfuns
560 -~sci-R/R_utils :: R.utils
561 -
562 -~sci-R/Sim_DiffProc :: Sim.DiffProc
563 -~sci-R/SNPMaP_cdm :: SNPMaP.cdm
564 -~sci-R/survJamda_data :: survJamda.data
565 -
566 -~sci-R/tawny_types :: tawny.types
567 -
568 -~sci-R/DO_db :: DO.db
569 -~sci-R/IlluminaHumanMethylation27k_db :: IlluminaHumanMethylation27k.db
570 -~sci-R/IlluminaHumanMethylation450k_db :: IlluminaHumanMethylation450k.db
571 -~sci-R/KEGG_db :: KEGG.db
572 -~sci-R/SNPlocs_Hsapiens_dbSNP_20090506 :: SNPlocs.Hsapiens.dbSNP.20090506
573 -~sci-R/SNPlocs_Hsapiens_dbSNP_20100427 :: SNPlocs.Hsapiens.dbSNP.20100427
574 -~sci-R/SNPlocs_Hsapiens_dbSNP_20101109 :: SNPlocs.Hsapiens.dbSNP.20101109
575 -~sci-R/gahgu133plus2_db :: gahgu133plus2.db
576 -~sci-R/hgfocus_db :: hgfocus.db
577 -~sci-R/hgu133a_db :: hgu133a.db
578 -~sci-R/hgu133plus2_db :: hgu133plus2.db
579 -~sci-R/hgu95a_db :: hgu95a.db
580 -~sci-R/hgu95av2_db :: hgu95av2.db
581 -~sci-R/hgug4112a_db :: hgug4112a.db
582 -~sci-R/hu6800_db :: hu6800.db
583 -~sci-R/illuminaHumanv1_db :: illuminaHumanv1.db
584 -~sci-R/nutshell_bbdb :: nutshell.bbdb
585 -~sci-R/reactome_db :: reactome.db
586 -
587 -~sci-R/RmiR_Hs_miRNA :: RmiR.Hs.miRNA
588 -~sci-R/TxDb_Hsapiens_UCSC_hg18_knownGene :: TxDb.Hsapiens.UCSC.hg18.knownGene
589 -~sci-R/TxDb_Hsapiens_UCSC_hg19_knownGene :: TxDb.Hsapiens.UCSC.hg19.knownGene
590 -~sci-R/bigmemory_sri :: bigmemory.sri
591 -~sci-R/gamlss_add :: gamlss.add
592 -~sci-R/gemtc_jar :: gemtc.jar
593 -~sci-R/haplo_stats :: haplo.stats
594 -~sci-R/nutshell_audioscrobbler :: nutshell.audioscrobbler
595 -~sci-R/pd_charm_hg18_example :: pd.charm.hg18.example
596 -~sci-R/pd_mapping250k_nsp :: pd.mapping250k.nsp
597 -~sci-R/pd_mapping250k_sty :: pd.mapping250k.sty
598 -~sci-R/pd_mapping50k_hind240 :: pd.mapping50k.hind240
599 -~sci-R/pd_mapping50k_xba240 :: pd.mapping50k.xba240
600 -~sci-R/simdat_base :: simdat.base
601 -
602
603 diff --git a/config/simple-deprules.d/ignored_text b/config/simple-deprules.d/ignored_text
604 index 097f004..b05353d 100644
605 --- a/config/simple-deprules.d/ignored_text
606 +++ b/config/simple-deprules.d/ignored_text
607 @@ -2,78 +2,53 @@
608
609 # ignored text
610 ! {
611 - available at <http://csound.sourceforge.net/>. See<http://playitbyr.org/csound.html> for more guidance on settingup Csound.
612 - available at<http://csound.sourceforge.net/>. This package uses the sharedlibrary file
613 - becauseBRugs does not support other platforms/OS right now.
614 - binary Linux distributions often package thelibrary separately from the executible file
615 - it is an extension for the R package tcltk that consists of Tclscripts. See README file.
616 - all other functions are stand alone)
617 - see also the topic 'SoPhy' in the documentation
618 - see also the topic'SoPhy' in the documentation
619 - see file README
620 - see README
621 - see README.
622 - see ./README.
623 - see the cloudRmpi manual (vignette)for details.
624 + does not support
625 + all other functions are stand alone
626 + documentation
627 + README
628 + INSTALL
629 + so for instance
630 + optional
631 + suggested
632 + See the
633 see topic SoPhy below
634 - so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration.
635 - so for instance onDebian and Ubuntu you would need the "libcsound64-dev" package.See the web site below for more guidance on setup.
636 some Windows variants are supported experimentally
637 - your mileage may vary)
638 - optional)
639 - heavily suggested)
640 - and Windows
641 - hence Windows or Linux
642 - $distributions package thelibrary file separately from the executible
643 - libraries(See the INSTALL file)
644 - or INSTALL.windows under Windows
645 - standard unix tools (e.g.
646 - rgdal OSX binary packages are also available at the samesite.
647 - rgdal OSX binary packages are also available at the same site.
648 - probably)
649 - Linux and Mac
650 - MPICH2 (>= 1.4.1p1) on Windows
651 + your mileage may vary
652 + Windows
653 + distributions package
654 + distributions often package
655 + probably
656 which is included with standard Mac and Windowsinstallations of Csound. Some Linux distributions package thelibrary file separately from the executible
657 - playitbyr creates sound using the csound package
658 - which requires the free and open source software synthesizerCsound
659 - A valid copy of the Csound library must present.Csound can be downloaded Thelibrary is included in the Windows and Mac OS X binaries
660 - A valid copy of the Csound library must present.Csound can be downloaded Thelibrary is included in the Windows
661 binary Linux distributions often package the library separatelyfrom the executible file
662 - so for instance on Debian and Ubuntuyou would need the "libcsound64-dev" package.
663 For the MERLIN wrapper
664 + Debian
665 + Ubuntu
666 Mac
667 - Mac OSX
668 - Mac OS X
669 - Mac OS X binaries
670 - Mac.Parallel HDF5
671 + OSX
672 + OS X
673 Linux/64bit
674 sources are included for other OSes.
675 see readme.txt
676 - so for instance on Debian
677 - so for instance onDebian
678 - Ubuntu you would need the "libcsound64-dev" package.See the package web site for more guidance on setup andconfiguration.
679 - Ubuntuyou would need the "libcsound64-dev" package.
680 - which is included with standard Mac
681 + so for instance
682 + you would need the
683 which requires the free
684 - drivers.
685 + drivers
686 License
687 its development files
688 - library (version2.2.0 or later)
689 - libraries(See README.REQ)
690 - Google Chrome for Windows
691 + ^library
692 + Google Chrome
693 for externalization
694 writing some graphicformats
695 - available athttp://www.monetdb.org
696 - it is used in the demos too).
697 + available at
698 + it is used in the demos too
699 headers
700 - OpenCSW.
701 + OpenCSW
702 + Linux
703 + precision AMD or Nvidia GPU
704 + ^and$
705 + in addition
706 }
707
708 -# that's a hardware requirement
709 -! :: double-precision AMD or Nvidia GPU
710 -
711 -% :: Linux
712 -
713 # ignore "Windows" in dependency fields:
714 # (a) there's OS_Type for OS restrictions
715 # (b) it's a filler word sometimes ("xyz on Solaris, Linux and Windows")
716 @@ -89,28 +64,12 @@
717 ! :: None
718
719 ! {
720 - Will use djmrgl or rgl packages for rendering ifpresent
721 - Will use djmrgl or rgl packages for rendering if present
722 - SYMPHONY for Windows (sources included for otherOSes)
723 + Will use djmrgl or rgl packages for rendering
724 SYMPHONY libraries
725 }
726
727 -# ignore OSX recommendations
728 -! {
729 - GDAL OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX
730 - GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX
731 - GDAL OSXframeworks built by William Kyngesburye athttp://www.kyngchaos.com/ may be used for source installs onOSX.
732 -}
733 -
734 -! {
735 - GEOS OSX frameworks built byWilliam Kyngesburye at http://www.kyngchaos.com/ may be usedfor source installs on OSX.
736 -}
737 -
738 # SoPhy splits its Depends field into windows and linux
739 ! {
740 - windows:Tiff for windows
741 - windows: Tiff (libtiff3.dll)
742 - windows: Tiff(libtiff3.dll)
743 zlib1.dll and jpeg62.dll
744 }
745
746
747 diff --git a/config/simple-deprules.d/media b/config/simple-deprules.d/media
748 index 41d8a03..3392d87 100644
749 --- a/config/simple-deprules.d/media
750 +++ b/config/simple-deprules.d/media
751 @@ -12,7 +12,7 @@ media-sound/csound {
752
753 #deptype all
754 media-gfx/imagemagick {
755 - Image Magick (for reading non PPM format)
756 + Image Magick
757 }
758 #deptype sys
759
760 @@ -23,25 +23,15 @@ media-gfx/graphviz :: dot from graphviz
761 }
762
763 media-gfx/swftools {
764 - SWF Tools (http://swftools.org) forsaveSWF()
765 - SWF Tools (http://swftools.org) for saveSWF()
766 + SWF.*Tools
767 }
768
769 virtual/ffmpeg {
770 - FFmpeg (http://ffmpeg.org) for saveVideo()
771 - FFmpeg(http://ffmpeg.org) for saveVideo()
772 ffmpeg
773 }
774
775 -media-gfx/dcraw {
776 - dcraw(for reading RAW images).
777 - dcraw (for readingRAW images).
778 -}
779 +media-gfx/dcraw :: dcraw
780
781 -media-libs/fontconfig {
782 - fontconfig
783 -}
784 +media-libs/fontconfig :: fontconfig
785
786 -media-fonts/corefonts {
787 - msttcorefonts
788 -}
789 +media-fonts/corefonts :: msttcorefonts
790
791 diff --git a/config/simple-deprules.d/media-libs b/config/simple-deprules.d/media-libs
792 index 8b7ba10..799335f 100644
793 --- a/config/simple-deprules.d/media-libs
794 +++ b/config/simple-deprules.d/media-libs
795 @@ -3,23 +3,15 @@
796 ~media-libs/flac :: flac
797
798 # FIXME: some packages write optional deps into SystemRequirements (e.g. rgl from CRAN)
799 -media-libs/freetype :: FreeType (optional)
800 ~media-libs/freetype :: freetype
801 media-libs/freetype:2 :: recommended: freetype2
802
803 -media-libs/gd {
804 - libgd (>= 2.0.28 http://www.boutell.com/gd/)
805 - libgd (>= 2.0.29 http://www.boutell.com/gd/)
806 - libgd (freetype2
807 -}
808 +media-libs/gd :: libgd
809 +
810 +media-libs/libpng :: libpng
811
812 -media-libs/libpng {
813 - libpng(>=1.2.9
814 - libpng (optional)
815 - libpng(optional)
816 -}
817 ~media-libs/libpng {
818 - png
819 + png$
820 libpng
821 }
822
823 @@ -27,13 +19,9 @@ media-libs/libpng {
824
825 ~media-libs/netpbm :: netpbm
826
827 -media-libs/raptor :: libraptor2 (>= 2.0.0 http://librdf.org/raptor/)
828 +media-libs/raptor :: libraptor
829
830 -media-libs/tiff {
831 - linux: libtiff (and libtiff-devel)
832 - optional libtiff
833 - optionally libtiff
834 -}
835 +media-libs/tiff :: libtiff
836
837 ~media-libs/tiff {
838 tiff
839 @@ -41,8 +29,4 @@ media-libs/tiff {
840 libtiff-devel
841 }
842
843 -virtual/jpeg {
844 - libjpeg
845 - jpeg
846 - jpeg libraries
847 -}
848 +virtual/jpeg :: jpeg
849
850 diff --git a/config/simple-deprules.d/misc b/config/simple-deprules.d/misc
851 index 9157f64..f403705 100644
852 --- a/config/simple-deprules.d/misc
853 +++ b/config/simple-deprules.d/misc
854 @@ -1,9 +1,7 @@
855 -dev-vcs/git {
856 - git
857 -}
858 +dev-vcs/git :: ^git$
859
860 >=app-emulation/wine-1.5.26 {
861 - wine (>= wine-1.5.26)
862 + wine.*1.5.26
863 }
864
865
866
867 diff --git a/config/simple-deprules.d/net b/config/simple-deprules.d/net
868 index ab87ea8..a2e6184 100644
869 --- a/config/simple-deprules.d/net
870 +++ b/config/simple-deprules.d/net
871 @@ -1,31 +1,20 @@
872 #deptype sys
873
874 -net-misc/curl {
875 - curl (version 7.12.0) http://curl.haxx.se
876 - curl (version 7.12.0 or higher)<http://curl.haxx.se>
877 - curl (version 7.12.0 or higher) http://curl.haxx.se
878 - curl (version 7.12.0 or higher) <http://curl.haxx.se>
879 - curl (version 7.14.0 or higher) http://curl.haxx.se
880 - you will often have toexplicitly install libcurl-devel to have the header files andthe libcurl library.
881 - libcurl (version 7.14.0 or higher)http://curl.haxx.se. On Linux systems
882 - you will oftenhave to explicitly install libcurl-devel to have theheader files
883 - libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb).
884 -}
885 +net-misc/curl :: curl
886 ~net-misc/curl {
887 curl
888 libcurl
889 - the libcurl library.
890 + the libcurl library
891 }
892
893 # FIXME
894 net-libs/czmq :: libzmq
895
896 -net-libs/zeromq {
897 - or ZeroMQ library >=4.0.4. Solaris 10 needs ZeroMQ library 4.0.7
898 -}
899 +net-libs/zeromq :: ZeroMQ
900
901 net-misc/s3cmd :: s3cmd
902
903 virtual/ssh {
904 - ssh daemon on the server side only:see the rreval manual (vignette) for details.
905 + ^ssh
906 + ssh$
907 }
908
909 diff --git a/config/simple-deprules.d/nvidia b/config/simple-deprules.d/nvidia
910 index ed77098..69a5775 100644
911 --- a/config/simple-deprules.d/nvidia
912 +++ b/config/simple-deprules.d/nvidia
913 @@ -2,34 +2,24 @@
914
915 # lowest cuda version in portage is 4.2.9
916 dev-util/nvidia-cuda-toolkit {
917 - NVIDIA CUDA Toolkit (>= release 3.0)
918 - Nvidia CUDAToolkit (>= release 3.0)
919 - Nvidia's CUDA toolkit (>= release 2.3)
920 - NVIDIA CUDA Toolkit 3.1 or above
921 - NVIDIA CUDAtoolkit
922 - NVIDIA CUDA Toolkit (>= release 4.0)
923 + NVIDIA.*CUDA.*Toolkit
924 }
925
926 >=dev-util/nvidia-cuda-toolkit-5.0 {
927 - Nvidia's CUDA toolkit (>= release 5.0)
928 + Nvidia's CUDA toolkit.*5.0
929 }
930
931 # FIXME cuda-toolkit or sdk?
932 dev-util/nvidia-cuda-toolkit {
933 - nvcc (>= release 2.1)
934 - nvcc (>= release 2.1) nVidia GPU (compute number >=1.3)
935 - nvcc (release 2.3) NVIDIA Cuda Compiler driver
936 - nvcc (release 3.0) NVIDIA Cuda Compiler driver
937 - nvcc (release >= 3.1) (NVIDIA Cuda Compilerdriver)
938 - nvcc release 3.1 (NVIDIA Cuda Compiler driver)
939 + nvcc
940 }
941
942 >=dev-util/nvidia-cuda-toolkit-4.1 {
943 - Nvidia's CUDA toolkit (release >= 4.1)
944 + Nvidia's CUDA toolkit.*4.1
945 }
946
947 >=dev-util/nvidia-cuda-toolkit-4.5 {
948 - Nvidia's CUDA toolkit (>= release 4.5)
949 + Nvidia's CUDA toolkit.*4.5
950 }
951
952 ~dev-util/nvidia-cuda-toolkit {
953 @@ -37,5 +27,5 @@ dev-util/nvidia-cuda-toolkit {
954 }
955
956 >=x11-drivers/nvidia-drivers-270 {
957 - Nvidia CUDA driver (>= 270.xx.xx)
958 + Nvidia CUDA driver.*270
959 }
960
961 diff --git a/config/simple-deprules.d/sci b/config/simple-deprules.d/sci
962 index 70521d9..6a93b72 100644
963 --- a/config/simple-deprules.d/sci
964 +++ b/config/simple-deprules.d/sci
965 @@ -2,8 +2,7 @@
966
967 # == geo ==
968 ~sci-geosciences/gmt {
969 - libgmt
970 - gmt
971 + gmt$
972 }
973 ~sci-geosciences/grass :: grass
974
975 @@ -11,44 +10,35 @@
976
977 ~sci-mathematics/glpk {
978 glpk
979 - GLPK library package (e.g.
980 }
981
982 ~sci-mathematics/jags :: jags
983 -sci-mathematics/jags :: jags (see http://mcmc-jags.sourceforge.net)
984 -
985 -sci-mathematics/jags {
986 - JAGS (>= 3.2.0) (or WinBUGS (>= 1.4) or OpenBUGS(>= 3.2.2))
987 -}
988
989 # lowest octave version in portage is 3.4
990 sci-mathematics/octave {
991 - Octave (>= 3.2.4) and its development files
992 + Octave
993 }
994
995 # lowest version in portage is 2.3.4-r1
996 sci-mathematics/pari {
997 - PARI/GP >= 2.3.0 [strongly recommended for logkda()]
998 - PARI/GP >= 2.3.0 [strongly recommended forlogkda()]
999 pari/gp
1000 }
1001
1002 sci-mathematics/singular {
1003 - Singular (http://www.singular.uni-kl.de) for exactcalculation of the MFR for graphs without splitting edges (onlyfor Unix systems).
1004 + Singular
1005 }
1006
1007 ~sci-mathematics/yacas :: yacas
1008 sci-mathematics/yacas {
1009 - yacas (= 1.0.63) # instructions on home page
1010 - yacas (>= 1.0.63) # instructions on home page
1011 + yacas
1012 }
1013
1014 sci-mathematics/octave {
1015 - Octave (>= 3.2.4)
1016 + Octave
1017 }
1018
1019 sci-libs/netcdf {
1020 - NetCDF4 (4.1 or later) libraries.
1021 + NetCDF4
1022 }
1023
1024 # there's also sci-biology/clustalw-mpi
1025 @@ -58,8 +48,8 @@ sci-biology/clustalw {
1026 }
1027
1028 sci-biology/ncbi-tools++ {
1029 - ncbi-blast+
1030 - ncbi-tools++
1031 + ncbi-blast\+
1032 + ncbi-tools\+\+
1033 }
1034
1035 sci-biology/kalign {
1036 @@ -67,13 +57,13 @@ sci-biology/kalign {
1037 }
1038
1039 sci-mathematics/glpk {
1040 - libglpk-dev onDebian/Ubuntu)
1041 + libglpk-dev
1042 }
1043
1044 #deptype all
1045
1046 # some packages have glpk in "pkg" deps
1047 -# (FIXME: does glpk in that context refer to an R package?)
1048 +# FIXME: does glpk in that context refer to an R package?
1049 ~sci-mathematics/glpk {
1050 glpk
1051 }
1052 @@ -94,14 +84,14 @@ sci-mathematics/rstudio {
1053
1054 # lowest sci-physics/root version in portage is 5.32.03
1055 sci-physics/root {
1056 - root_v5.32.01 <http://root.cern.ch> - See READMEfile for installation instructions.
1057 + root_v5.32.01
1058 }
1059
1060 # == visualization ==
1061
1062 ~sci-visualization/ggobi :: ggobi
1063
1064 -sci-biology/merlin :: MERLIN(www.sph.umich.edu/csg/abecasis/merlin) must be installed andpointed to in the PATH environment variable.
1065 +sci-biology/merlin :: MERLIN
1066
1067 sci-visualization/gnuplot {
1068 gnuplot
1069
1070 diff --git a/config/simple-deprules.d/sci-libs b/config/simple-deprules.d/sci-libs
1071 index 14da6a3..45506a8 100644
1072 --- a/config/simple-deprules.d/sci-libs
1073 +++ b/config/simple-deprules.d/sci-libs
1074 @@ -8,15 +8,13 @@
1075 # Use slot when the resolver can deal with them properly
1076 >=sci-libs/fftw-3 {
1077 fftw3
1078 - fftw3 (optional)
1079 }
1080 ~sci-libs/fftw :: fftw
1081 # Use slot when the resolver can deal with them properly
1082 ~sci-libs/fftw :: fftw3
1083
1084 sci-libs/gdal {
1085 - GDAL library from http://www.gdal.org/download.html
1086 - GDAL library from http://www.remotesensing.org/gdal/download.html
1087 + GDAL library
1088
1089 }
1090 ~sci-libs/gdal {
1091 @@ -30,37 +28,29 @@ sci-libs/gdal {
1092 }
1093
1094 sci-libs/gsl {
1095 - gsl. Note: users should have GSL installed. Windowsusers: 'consult the README file available in the inst directoryof the source distribution for necessary configurationinstructions'.
1096 - gsl (with development libraries)
1097 + ^gsl
1098 }
1099 ~sci-libs/gsl {
1100 GNU GSL
1101 - gsl
1102 + ^gsl
1103 libgsl
1104 - libgslcblas
1105 - GNU GSL for the GSL random-number generators
1106 - GNU GSL forthe GSL random-number generators
1107 - GNU Scientific Library (GSL)
1108 - GNU Scientific Library version
1109 + GNU Scientific Library
1110 }
1111
1112 ~sci-libs/hdf5 :: hdf5
1113 sci-libs/hdf5[cxx] {
1114 - libhdf5 (>= 1.8.x) with C++ interface(--enable-cxx=yes)
1115 - libhdf5 (>= 1.8.12) with C++ interface(--enable-cxx=yes)
1116 + libhdf5.*C\+\+
1117 }
1118 # remnant of hdf5
1119 ! :: v18 API enabled
1120
1121 ~sci-libs/itpp {
1122 - itpp
1123 - libitpp
1124 + itpp$
1125 }
1126
1127 # FIXME: dev-lang/R[lapack]?
1128 virtual/lapack {
1129 - LAPACK sharedlibrary
1130 - LAPACKshared library
1131 + LAPACK
1132 }
1133
1134 sci-libs/lapack-atlas :: lapack_atlas
1135 @@ -70,19 +60,12 @@ sci-libs/libsvm :: SVMlight
1136
1137 ~sci-libs/mkl :: Intel MKL
1138
1139 -sci-libs/netcdf :: netcdf library version 4.1 or later
1140 ~sci-libs/netcdf :: netcdf
1141
1142 -sci-libs/proj :: proj 4.4.6 or higher (http://proj.maptools.org/)
1143 ->=sci-libs/proj-4.4.9 :: PROJ.4(proj >= 4.4.9)
1144 -
1145 +sci-libs/proj :: ^proj
1146
1147 # FIXME, portage version is 2.1.21
1148 -sci-libs/udunits :: udunits (>= 1.11.7) or udunits2(>= 2.1.22)
1149 -~sci-libs/udunits {
1150 - udunits
1151 - udunits-2
1152 -}
1153 +sci-libs/udunits :: udunits
1154
1155 virtual/blas :: blas
1156
1157
1158 diff --git a/config/simple-deprules.d/selfdeps b/config/simple-deprules.d/selfdeps
1159 deleted file mode 100644
1160 index 63e49bc..0000000
1161 --- a/config/simple-deprules.d/selfdeps
1162 +++ /dev/null
1163 @@ -1,22 +0,0 @@
1164 -#! NOPARSE
1165 -#! ERROR
1166 -# Replaced by the selfdeps.d directory, which contains per-repo selfdep files.
1167 -#
1168 -# This file lists old rules, which are not yet included there.
1169 -#
1170 -
1171 -#deptype pkg,selfdep
1172 -
1173 -sci-R/chron :: get.hist.quote needs packagechron.
1174 -
1175 -# FIXME: correct?
1176 -~sci-R/CoCo {
1177 - CoCoCore
1178 - CoCoObjects
1179 - CoCoRaw
1180 -}
1181 -sci-R/survival4 :: survival4 if survival models are to be used.
1182 -~sci-R/survival5 :: survival5 for some examples
1183 -sci-R/survival5 :: survival5 if survival models are to be used.
1184 -
1185 -~sci-R/VhayuR :: Vhayu
1186
1187 diff --git a/config/simple-deprules.d/selfdeps.d/sci-CRAN b/config/simple-deprules.d/selfdeps.d/sci-CRAN
1188 index 5935939..0994353 100644
1189 --- a/config/simple-deprules.d/selfdeps.d/sci-CRAN
1190 +++ b/config/simple-deprules.d/selfdeps.d/sci-CRAN
1191 @@ -1,30 +1,29 @@
1192 #deptype pkg,selfdep
1193
1194 sci-CRAN/csound {
1195 - A valid copy of the Csound library must be present.Csound can be downloaded from http://www.csounds.com. Thelibrary is included in the default Windows and Mac OS Xdistributions
1196 - playitbyr creates sound using the csound package
1197 - which requires the free and open source software synthesizerCsound
1198 + Csound
1199 }
1200
1201 -~sci-CRAN/mimR :: mim
1202 +# IRKernel has a conflicting named sci-R/repr.
1203 +~sci-CRAN/repr :: ^repr$
1204 +
1205 +~sci-CRAN/mimR :: ^mim$
1206
1207 sci-CRAN/quadprog :: portfolio.optim needs package quadprog
1208
1209 sci-CRAN/rgl :: rgl packages for rendering
1210
1211 sci-CRAN/MVA {
1212 - white.test needs packagemva
1213 - white.test needs package mva
1214 + package.*mva
1215 }
1216
1217 ~sci-CRAN/sgeostat {
1218 - sgeostat.
1219 - geostat.
1220 + geostat
1221 }
1222
1223 # the following rule is _not_ correct
1224 -# (the dependency strings listed here want the "xgobi" program from
1225 -# http://www.research.att.com/areas/stat/xgobi/, not the R package)
1226 +# the dependency strings listed here want the "xgobi" program from
1227 +# http://www.research.att.com/areas/stat/xgobi/, not the R package
1228 #
1229 ## sci-CRAN/xgobi {
1230 ## xgobi must be installed additionally
1231 @@ -33,8 +32,6 @@ sci-CRAN/MVA {
1232
1233 ~sci-CRAN/BayesFactor :: BayesFactorPCL
1234
1235 ->=sci-CRAN/adimpro-0.4.2 :: adimpro (>= 0.4.2)The R-package 'adimpro' (for reading
1236 -
1237 sci-CRAN/adimpro {
1238 - The R-package 'adimpro' (for reading
1239 + adimpro
1240 }
1241
1242 diff --git a/config/simple-deprules.d/sys b/config/simple-deprules.d/sys
1243 index b2fa9bd..88ddb06 100644
1244 --- a/config/simple-deprules.d/sys
1245 +++ b/config/simple-deprules.d/sys
1246 @@ -2,25 +2,19 @@
1247
1248 ~sys-libs/db {
1249 BerkelyDB
1250 - BerkeleyDB
1251 - Oracle Berkeley DB 11gR2
1252 + Berkeley.*DB
1253 }
1254
1255 ~sys-libs/zlib :: zlib
1256 -sys-libs/zlib :: zlib (optional)
1257
1258 # => sys-cluster/
1259 virtual/mpi {
1260 - LamMPI(>= 6.5.9) or MPICH2(>= 1.0.2) or OpenMPI ()
1261 - LamMpi(>= 6.5.9) or Mpich2(>= 1.0.2)
1262 - OpenMPI (>= 1.5.4) on Linux
1263 - OpenMPI or MPICH2
1264 -}
1265 -
1266 -# the "... on Windows" line could probably be ignored
1267 -virtual/mpi {
1268 + LamMPI
1269 + Open.*MPI
1270 + MPICH2
1271 MPI2
1272 - MPICH2 (>=1.4.1p1) on Windows
1273 + MPICH2
1274 + MPI.*library
1275 }
1276
1277 ! {
1278 @@ -32,17 +26,15 @@ virtual/mpi {
1279 ~sci-R/Rcpp :: Rcpp
1280
1281 # Split across multiple lines, next line adds Linux and Mac
1282 ->=sys-cluster/openmpi-1.5.4 :: OpenMPI (>= 1.5.4) on Solaris
1283 +>=sys-cluster/openmpi-1.5.4 :: OpenMPI
1284
1285 @selfdep
1286 -sci-R/rJava :: JRI
1287 -
1288 -~app-text/pandoc :: Pandoc (http://johnmacfarlane.net/pandoc) forexporting markdown files to other formats.
1289 +sci-R/rJava :: ^JRI$
1290
1291 ->=dev-tcltk/tktable-2.9 :: Tktable (>= 2.9
1292 +~dev-tcltk/tktable :: Tktable
1293
1294 ->=app-text/aspell-0.60 :: aspell (>= 0.60
1295 +~app-text/aspell :: aspell
1296
1297 -dev-libs/openssl :: OpenSSL library
1298 +dev-libs/openssl :: OpenSSL
1299
1300 -~app-crypt/dieharder :: DieHarder library
1301 +~app-crypt/dieharder :: DieHarder
1302
1303 diff --git a/config/simple-deprules.d/system.set b/config/simple-deprules.d/system.set
1304 index 54fc6a5..1e9b3e8 100644
1305 --- a/config/simple-deprules.d/system.set
1306 +++ b/config/simple-deprules.d/system.set
1307 @@ -2,43 +2,26 @@
1308
1309 # @system
1310 ! {
1311 + bash
1312 + ^awk$
1313 + gmake
1314 GNU make
1315 - GNU Make
1316 - GNU Make forexternalization
1317 - andg++ GNU compiler (a nvcc-compatible version of g++ is needed
1318 - andg++ GNU compiler version 3.4 (version 4.4 is not yet compatiblewith nvcc).
1319 - chmod)
1320 -}
1321 -
1322 -% :: gcc
1323 -# FIXME: newer gcc versions could work, too
1324 -<sys-devel/gcc-4.4 :: gcc/g++ version 4.4 is not yet compatible with nvcc).
1325 -<=sys-devel/gcc-4.5 :: gcc (release <= 4.5).
1326 -
1327 -#sys-devel/gcc[cxx] :: g++ or Microsoft VC++
1328 -! :: g++ or Microsoft VC++
1329 -! {
1330 - g++-4.6.* or later should be sufficient
1331 - g++-4.9.* or lateris preferred.
1332 - gcc (release >= 4.5).
1333 - C++11
1334 - C++11 (supporting at least std=c++0x)
1335 - A C++11 compiler. Version 4.6.* of g++ (ascurrently in Rtools) is insufficient
1336 + g\+\+ GNU compiler
1337 + chmod
1338 + ^gcc
1339 + ^g\+\+
1340 + ^C\+\+11
1341 + C\+\+11.*compiler
1342 }
1343
1344 # always provided? (except for Gentoo/*BSD)
1345 ! {
1346 - Linux operating system
1347 - Linux operating system.
1348 - Linuxoperationg system
1349 + Linux.*operating.*system
1350 }
1351 # always provided
1352 ! {
1353 - POSIX-compliant OS (essentially anything but Windows)
1354 - POSIX-compliant OS (essentially anything butWindows
1355 - POSIX-compliant OS (essentially anything butWindows)
1356 + POSIX.*OS
1357 Unix
1358 - A 64-bit POSIX OS such as Linux or OS X with IANAtime zone data in /usr/share/zoneinfo as well as a C++11compiler.
1359 }
1360
1361 # rpcgen is part of glibc
1362
1363 diff --git a/config/simple-deprules.d/unknown b/config/simple-deprules.d/unknown
1364 index 8d1549d..04d20b6 100644
1365 --- a/config/simple-deprules.d/unknown
1366 +++ b/config/simple-deprules.d/unknown
1367 @@ -2,7 +2,6 @@
1368
1369 # FIXME: which library is meant?
1370 ! {
1371 - A C library with the fesetround/fegetroundfunctions.
1372 - library.
1373 - library
1374 + ^C.*library
1375 + ^library
1376 }
1377
1378 diff --git a/config/simple-deprules.d/x11 b/config/simple-deprules.d/x11
1379 index 2858ddd..ff93d39 100644
1380 --- a/config/simple-deprules.d/x11
1381 +++ b/config/simple-deprules.d/x11
1382 @@ -1,26 +1,22 @@
1383 #deptype sys
1384
1385 -x11-libs/cairo :: cairo (>= 1.2 http://www.cairographics.org/)
1386 ~x11-libs/cairo :: cairo
1387
1388 -~x11-libs/gtk+ :: gtk+
1389 +~x11-libs/gtk+ :: gtk\+
1390
1391 ~x11-libs/pango :: pango
1392
1393 # qt has its own category now
1394 dev-qt/qtcore {
1395 - qt
1396 - Qt4 libraries and headers (http://qt.nokia.com)
1397 - Qt4 libraries
1398 + ^qt$
1399 + ^Qt4.*libraries
1400 }
1401 -! :: headers (http://qt.nokia.com)
1402
1403 x11-misc/xclip {
1404 - xclip (Linux)
1405 + xclip
1406 }
1407
1408 virtual/opencl {
1409 - OpenCL library
1410 OpenCl
1411 }
1412
1413
1414 diff --git a/roverlay/depres/simpledeprule/abstractrules.py b/roverlay/depres/simpledeprule/abstractrules.py
1415 index d31ffbe..a1d8522 100644
1416 --- a/roverlay/depres/simpledeprule/abstractrules.py
1417 +++ b/roverlay/depres/simpledeprule/abstractrules.py
1418 @@ -8,7 +8,7 @@
1419
1420 __all__ = [ 'FuzzySimpleRule', 'SimpleRule', ]
1421
1422 -import logging
1423 +import logging, re
1424
1425 from roverlay import config
1426 from roverlay.depres import deprule
1427 @@ -21,7 +21,7 @@ class SimpleRule ( deprule.DependencyRule ):
1428 INDENT = 3 * ' '
1429
1430 def __init__ ( self,
1431 - dep_str=None, priority=50, resolving_package=None,
1432 + dep_str=None, priority=80, resolving_package=None,
1433 is_selfdep=0, logger_name='simple_rule',
1434 selfdep_package_names=None, finalize=False,
1435 ):
1436 @@ -67,6 +67,10 @@ class SimpleRule ( deprule.DependencyRule ):
1437 self.dep_alias = frozenset ( self.dep_alias )
1438 if self.prepare_lowercase_alias:
1439 self.dep_alias_low = frozenset ( x.lower() for x in self.dep_alias )
1440 + temp_set = self.dep_alias_low
1441 + if self.is_selfdep:
1442 + temp_set = ("^{}$".format(x) for x in self.dep_alias_low)
1443 + self.dep_regex = re.compile('|'.join(x for x in temp_set))
1444
1445 def add_resolved ( self, dep_str ):
1446 """Adds an dependency string that should be matched by this rule.
1447 @@ -80,7 +84,7 @@ class SimpleRule ( deprule.DependencyRule ):
1448 def _find ( self, dep_str, lowercase ):
1449 if lowercase:
1450 if hasattr ( self, 'dep_alias_low' ):
1451 - if dep_str in self.dep_alias_low:
1452 + if self.dep_regex.search(dep_str):
1453 return True
1454
1455 elif dep_str in ( alias.lower() for alias in self.dep_alias ):
1456
1457 diff --git a/roverlay/depres/simpledeprule/rules.py b/roverlay/depres/simpledeprule/rules.py
1458 index 869c5aa..12c6520 100644
1459 --- a/roverlay/depres/simpledeprule/rules.py
1460 +++ b/roverlay/depres/simpledeprule/rules.py
1461 @@ -151,11 +151,11 @@ class SimpleIgnoreDependencyRule ( SimpleRule ):
1462
1463 RULE_PREFIX = '!'
1464
1465 - def __init__ ( self, priority=50, resolving_package=None, **kw ):
1466 + def __init__ ( self, priority=80, resolving_package=None, **kw ):
1467 super ( SimpleIgnoreDependencyRule, self ) . __init__ (
1468 logger_name = 'IGNORE_DEPS',
1469 resolving_package=None,
1470 - priority=50,
1471 + priority=80,
1472 **kw
1473 )
1474 # --- end of SimpleIgnoreDependencyRule ---
1475 @@ -187,7 +187,7 @@ class SimpleFuzzyIgnoreDependencyRule ( FuzzySimpleRule ):
1476
1477 RULE_PREFIX = '%'
1478
1479 - def __init__ ( self, priority=51, resolving_package=None, **kw ):
1480 + def __init__ ( self, priority=81, resolving_package=None, **kw ):
1481 super ( SimpleFuzzyIgnoreDependencyRule, self ) . __init__ (
1482 priority=priority,
1483 resolving_package=resolving_package,