| 1 |
commit: eead4c719f1583683e0f7152b72c943e97e9a13d |
| 2 |
Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Mar 28 17:37:56 2015 +0000 |
| 4 |
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sat Mar 28 17:37:56 2015 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=eead4c71 |
| 7 |
|
| 8 |
Moved to tree, thanks Ted Tanberry for all the help |
| 9 |
|
| 10 |
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
| 11 |
|
| 12 |
sci-biology/embassy-cbstools/ChangeLog | 61 --- |
| 13 |
.../embassy-cbstools-1.0.0.650.ebuild | 13 - |
| 14 |
...bassy-cbstools-1.0.0.650_fix-build-system.patch | 97 ----- |
| 15 |
sci-biology/embassy-cbstools/metadata.xml | 5 - |
| 16 |
sci-biology/embassy-clustalomega/ChangeLog | 117 ------ |
| 17 |
.../embassy-clustalomega-1.1.0.ebuild | 15 - |
| 18 |
...bassy-clustalomega-1.1.0_fix-build-system.patch | 90 ----- |
| 19 |
sci-biology/embassy-clustalomega/metadata.xml | 5 - |
| 20 |
sci-biology/embassy-domainatrix/ChangeLog | 174 --------- |
| 21 |
.../embassy-domainatrix-0.1.650.ebuild | 13 - |
| 22 |
...assy-domainatrix-0.1.650_fix-build-system.patch | 91 ----- |
| 23 |
sci-biology/embassy-domainatrix/metadata.xml | 5 - |
| 24 |
sci-biology/embassy-domalign/ChangeLog | 118 ------ |
| 25 |
.../embassy-domalign-0.1.650.ebuild | 13 - |
| 26 |
...embassy-domalign-0.1.650_fix-build-system.patch | 92 ----- |
| 27 |
sci-biology/embassy-domalign/metadata.xml | 5 - |
| 28 |
sci-biology/embassy-domsearch/ChangeLog | 116 ------ |
| 29 |
.../embassy-domsearch-0.1.650.ebuild | 13 - |
| 30 |
...mbassy-domsearch-0.1.650_fix-build-system.patch | 91 ----- |
| 31 |
sci-biology/embassy-domsearch/metadata.xml | 5 - |
| 32 |
sci-biology/embassy-emnu/ChangeLog | 157 -------- |
| 33 |
.../embassy-emnu/embassy-emnu-1.05.650.ebuild | 17 - |
| 34 |
.../embassy-emnu-1.05.650_fix-build-system.patch | 127 ------- |
| 35 |
sci-biology/embassy-emnu/metadata.xml | 5 - |
| 36 |
sci-biology/embassy-esim4/ChangeLog | 160 -------- |
| 37 |
.../embassy-esim4/embassy-esim4-1.0.0.650.ebuild | 13 - |
| 38 |
.../embassy-esim4-1.0.0.650_fix-build-system.patch | 97 ----- |
| 39 |
sci-biology/embassy-esim4/metadata.xml | 5 - |
| 40 |
sci-biology/embassy-hmmer/ChangeLog | 166 --------- |
| 41 |
.../embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild | 15 - |
| 42 |
.../embassy-hmmer-2.3.2.650_fix-build-system.patch | 90 ----- |
| 43 |
sci-biology/embassy-hmmer/metadata.xml | 5 - |
| 44 |
sci-biology/embassy-iprscan/ChangeLog | 45 --- |
| 45 |
.../embassy-iprscan-4.3.1.650.ebuild | 13 - |
| 46 |
...mbassy-iprscan-4.3.1.650_fix-build-system.patch | 97 ----- |
| 47 |
sci-biology/embassy-iprscan/metadata.xml | 5 - |
| 48 |
sci-biology/embassy-meme/ChangeLog | 75 ---- |
| 49 |
.../embassy-meme/embassy-meme-4.7.650.ebuild | 15 - |
| 50 |
.../embassy-meme-4.7.650_fix-build-system.patch | 90 ----- |
| 51 |
sci-biology/embassy-meme/metadata.xml | 5 - |
| 52 |
sci-biology/embassy-mse/ChangeLog | 185 ---------- |
| 53 |
.../embassy-mse/embassy-mse-3.0.0.650.ebuild | 23 -- |
| 54 |
.../embassy-mse-3.0.0.650_fix-build-system.patch | 133 ------- |
| 55 |
sci-biology/embassy-mse/metadata.xml | 5 - |
| 56 |
sci-biology/embassy-phylipnew/ChangeLog | 81 ---- |
| 57 |
.../embassy-phylipnew-3.69.650.ebuild | 15 - |
| 58 |
...bassy-phylipnew-3.69.650_fix-build-system.patch | 98 ----- |
| 59 |
sci-biology/embassy-phylipnew/metadata.xml | 5 - |
| 60 |
sci-biology/embassy-signature/ChangeLog | 116 ------ |
| 61 |
.../embassy-signature-0.1.650.ebuild | 13 - |
| 62 |
...mbassy-signature-0.1.650_fix-build-system.patch | 90 ----- |
| 63 |
sci-biology/embassy-signature/metadata.xml | 5 - |
| 64 |
sci-biology/embassy-structure/ChangeLog | 116 ------ |
| 65 |
.../embassy-structure-0.1.650.ebuild | 13 - |
| 66 |
...mbassy-structure-0.1.650_fix-build-system.patch | 90 ----- |
| 67 |
sci-biology/embassy-structure/metadata.xml | 5 - |
| 68 |
sci-biology/embassy-topo/ChangeLog | 161 -------- |
| 69 |
.../embassy-topo/embassy-topo-2.0.650.ebuild | 13 - |
| 70 |
.../embassy-topo-2.0.650_fix-build-system.patch | 97 ----- |
| 71 |
sci-biology/embassy-topo/metadata.xml | 5 - |
| 72 |
sci-biology/embassy-vienna/ChangeLog | 65 ---- |
| 73 |
.../embassy-vienna/embassy-vienna-1.7.2.650.ebuild | 13 - |
| 74 |
...embassy-vienna-1.7.2.650_fix-build-system.patch | 98 ----- |
| 75 |
sci-biology/embassy-vienna/metadata.xml | 5 - |
| 76 |
sci-biology/embassy/ChangeLog | 160 -------- |
| 77 |
sci-biology/embassy/embassy-6.6.0.ebuild | 30 -- |
| 78 |
sci-biology/embassy/metadata.xml | 5 - |
| 79 |
sci-biology/emboss/ChangeLog | 407 --------------------- |
| 80 |
sci-biology/emboss/emboss-6.6.0.ebuild | 59 --- |
| 81 |
sci-biology/emboss/files/README.gentoo | 34 -- |
| 82 |
.../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch | 11 - |
| 83 |
.../files/emboss-6.6.0_fix-build-system.patch | 368 ------------------- |
| 84 |
.../files/emboss-6.6.0_plplot-declarations.patch | 61 --- |
| 85 |
.../emboss-6.6.0_qa-implicit-declarations.patch | 74 ---- |
| 86 |
sci-biology/emboss/metadata.xml | 18 - |
| 87 |
75 files changed, 5018 deletions(-) |
| 88 |
|
| 89 |
diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog |
| 90 |
deleted file mode 100644 |
| 91 |
index d7fb20f..0000000 |
| 92 |
--- a/sci-biology/embassy-cbstools/ChangeLog |
| 93 |
+++ /dev/null |
| 94 |
@@ -1,61 +0,0 @@ |
| 95 |
-# ChangeLog for sci-biology/embassy-cbstools |
| 96 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 97 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.5 2010/01/15 22:44:35 fauli Exp $ |
| 98 |
- |
| 99 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 100 |
- -embassy-cbstools-1.0.0-r3.ebuild, embassy-cbstools-1.0.0.650.ebuild, |
| 101 |
- -files/embassy-cbstools-1.0.0-r2.patch, metadata.xml: |
| 102 |
- Bump eclass, Drop old |
| 103 |
- |
| 104 |
-*embassy-cbstools-1.0.0-r3 (19 Sep 2011) |
| 105 |
- |
| 106 |
- 19 Sep 2011; Justin Lecher <jlec@g.o> |
| 107 |
- -embassy-cbstools-1.0.0-r2.ebuild, +embassy-cbstools-1.0.0-r3.ebuild: |
| 108 |
- Silent upstream bump |
| 109 |
- |
| 110 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 111 |
- embassy-cbstools-1.0.0-r2.ebuild: |
| 112 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 113 |
- |
| 114 |
- 19 Mar 2011; Justin Lecher <jlec@g.o> |
| 115 |
- embassy-cbstools-1.0.0-r2.ebuild, files/embassy-cbstools-1.0.0-r2.patch: |
| 116 |
- Fixed for reviewed eclass |
| 117 |
- |
| 118 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 119 |
- embassy-cbstools-1.0.0-r2.ebuild: |
| 120 |
- Naming of eclass changed |
| 121 |
- |
| 122 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 123 |
- embassy-cbstools-1.0.0-r2.ebuild: |
| 124 |
- EOV not needed to be set anymore |
| 125 |
- |
| 126 |
-*embassy-cbstools-1.0.0-r2 (10 Mar 2011) |
| 127 |
- |
| 128 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 129 |
- +embassy-cbstools-1.0.0-r2.ebuild, +files/embassy-cbstools-1.0.0-r2.patch, |
| 130 |
- +metadata.xml: |
| 131 |
- Move to new embassy-ng.eclass |
| 132 |
- |
| 133 |
- 15 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 134 |
- embassy-cbstools-1.0.0-r1.ebuild: |
| 135 |
- Transfer Prefix keywords |
| 136 |
- |
| 137 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 138 |
- Giving up maintainership of this package. |
| 139 |
- |
| 140 |
-*embassy-cbstools-1.0.0-r1 (01 Sep 2009) |
| 141 |
- |
| 142 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 143 |
- +embassy-cbstools-1.0.0-r1.ebuild: |
| 144 |
- Updated version for EMBASSY 6.1.0. |
| 145 |
- |
| 146 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 147 |
- embassy-cbstools-1.0.0.ebuild: |
| 148 |
- Stabilised on amd64 and x86. |
| 149 |
- |
| 150 |
-*embassy-cbstools-1.0.0 (27 Aug 2008) |
| 151 |
- |
| 152 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 153 |
- +embassy-cbstools-1.0.0.ebuild: |
| 154 |
- Initial import for EMBASSY 6.0.1. |
| 155 |
- |
| 156 |
|
| 157 |
diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild |
| 158 |
deleted file mode 100644 |
| 159 |
index a903ba3..0000000 |
| 160 |
--- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild |
| 161 |
+++ /dev/null |
| 162 |
@@ -1,13 +0,0 @@ |
| 163 |
-# Copyright 1999-2015 Gentoo Foundation |
| 164 |
-# Distributed under the terms of the GNU General Public License v2 |
| 165 |
-# $Header: $ |
| 166 |
- |
| 167 |
-EAPI=5 |
| 168 |
- |
| 169 |
-EBO_DESCRIPTION="applications from the CBS group" |
| 170 |
- |
| 171 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 172 |
-AUTOTOOLS_AUTORECONF=1 |
| 173 |
-inherit emboss-r1 |
| 174 |
- |
| 175 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
| 176 |
|
| 177 |
diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch |
| 178 |
deleted file mode 100644 |
| 179 |
index 63c67a1..0000000 |
| 180 |
--- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch |
| 181 |
+++ /dev/null |
| 182 |
@@ -1,97 +0,0 @@ |
| 183 |
---- CBSTOOLS-1.0.0.650/configure.ac |
| 184 |
-+++ CBSTOOLS-1.0.0.650/configure.ac |
| 185 |
-@@ -635,33 +635,6 @@ |
| 186 |
- |
| 187 |
- |
| 188 |
- |
| 189 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 190 |
--dnl to see which version's configure.in these lines come from |
| 191 |
-- |
| 192 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 193 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 194 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 195 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 196 |
--dnl that many releases anyway. |
| 197 |
-- |
| 198 |
--PCRE_MAJOR="7" |
| 199 |
--PCRE_MINOR="9" |
| 200 |
--PCRE_DATE="11-Apr-2009" |
| 201 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 202 |
-- |
| 203 |
--dnl Default values for miscellaneous macros |
| 204 |
-- |
| 205 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 206 |
-- |
| 207 |
--dnl Provide versioning information for libtool shared libraries that |
| 208 |
--dnl are built by default on Unix systems. |
| 209 |
-- |
| 210 |
--PCRE_LIB_VERSION="0:1:0" |
| 211 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 212 |
-- |
| 213 |
-- |
| 214 |
-- |
| 215 |
-- |
| 216 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 217 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 218 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 219 |
-@@ -737,21 +710,6 @@ |
| 220 |
- |
| 221 |
- |
| 222 |
- |
| 223 |
--dnl "Export" these variables for PCRE |
| 224 |
-- |
| 225 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 226 |
--AC_SUBST([HAVE_STRERROR]) |
| 227 |
--AC_SUBST([PCRE_MAJOR]) |
| 228 |
--AC_SUBST([PCRE_MINOR]) |
| 229 |
--AC_SUBST([PCRE_DATE]) |
| 230 |
--AC_SUBST([PCRE_VERSION]) |
| 231 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 232 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 233 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 234 |
-- |
| 235 |
-- |
| 236 |
-- |
| 237 |
-- |
| 238 |
- dnl Test if --enable-localforce given |
| 239 |
- locallink="no" |
| 240 |
- embprefix="/usr/local" |
| 241 |
-@@ -874,6 +832,11 @@ |
| 242 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 243 |
- |
| 244 |
- |
| 245 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 246 |
-+[ |
| 247 |
-+dnl using system libraries |
| 248 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 249 |
-+]) |
| 250 |
- |
| 251 |
- |
| 252 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 253 |
---- CBSTOOLS-1.0.0.650/src/Makefile.am |
| 254 |
-+++ CBSTOOLS-1.0.0.650/src/Makefile.am |
| 255 |
-@@ -19,9 +19,7 @@ |
| 256 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 257 |
- -I../../../ajax/acd -I../../../plplot |
| 258 |
- else |
| 259 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 260 |
-- $(NLINCLUDES) \ |
| 261 |
-- -I${embprefix}/include/epcre |
| 262 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 263 |
- endif |
| 264 |
- |
| 265 |
- if ISSHARED |
| 266 |
-@@ -65,5 +63,5 @@ |
| 267 |
- $(XLIB) |
| 268 |
- else |
| 269 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 270 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 271 |
-+ -lajax $(NLADD) $(XLIB) |
| 272 |
- endif |
| 273 |
---- CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am |
| 274 |
-+++ CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am |
| 275 |
-@@ -1,3 +1,3 @@ |
| 276 |
- |
| 277 |
--pkgdata_DATA = *.acd |
| 278 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 279 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 280 |
|
| 281 |
diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml |
| 282 |
deleted file mode 100644 |
| 283 |
index f17a827..0000000 |
| 284 |
--- a/sci-biology/embassy-cbstools/metadata.xml |
| 285 |
+++ /dev/null |
| 286 |
@@ -1,5 +0,0 @@ |
| 287 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 288 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 289 |
-<pkgmetadata> |
| 290 |
- <herd>sci-biology</herd> |
| 291 |
-</pkgmetadata> |
| 292 |
|
| 293 |
diff --git a/sci-biology/embassy-clustalomega/ChangeLog b/sci-biology/embassy-clustalomega/ChangeLog |
| 294 |
deleted file mode 100644 |
| 295 |
index 8d02254..0000000 |
| 296 |
--- a/sci-biology/embassy-clustalomega/ChangeLog |
| 297 |
+++ /dev/null |
| 298 |
@@ -1,117 +0,0 @@ |
| 299 |
-# ChangeLog for sci-biology/embassy-clustalomega |
| 300 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 301 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.20 2010/01/01 21:51:36 fauli Exp $ |
| 302 |
- |
| 303 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 304 |
- embassy-clustalomega-1.1.0.ebuild, metadata.xml: |
| 305 |
- Bump eclass |
| 306 |
- |
| 307 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 308 |
- embassy-domalign-0.1.0-r5.ebuild: |
| 309 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 310 |
- |
| 311 |
- 19 Mar 2011; Justin Lecher <jlec@g.o> |
| 312 |
- embassy-domalign-0.1.0-r5.ebuild, files/embassy-domalign-0.1.0-r5.patch: |
| 313 |
- Fixed for reviewed eclass |
| 314 |
- |
| 315 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 316 |
- embassy-domalign-0.1.0-r5.ebuild: |
| 317 |
- Naming of eclass changed |
| 318 |
- |
| 319 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 320 |
- embassy-domalign-0.1.0-r5.ebuild: |
| 321 |
- EOV not needed to be set anymore |
| 322 |
- |
| 323 |
-*embassy-domalign-0.1.0-r5 (10 Mar 2011) |
| 324 |
- |
| 325 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 326 |
- +embassy-domalign-0.1.0-r5.ebuild, +files/embassy-domalign-0.1.0-r5.patch, |
| 327 |
- +metadata.xml: |
| 328 |
- Move to new embassy-ng.eclass |
| 329 |
- |
| 330 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 331 |
- embassy-domalign-0.1.0-r4.ebuild: |
| 332 |
- Transfer Prefix keywords |
| 333 |
- |
| 334 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 335 |
- Giving up maintainership of this package. |
| 336 |
- |
| 337 |
-*embassy-domalign-0.1.0-r4 (01 Sep 2009) |
| 338 |
- |
| 339 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 340 |
- +embassy-domalign-0.1.0-r4.ebuild: |
| 341 |
- Updated version for EMBASSY 6.1.0. |
| 342 |
- |
| 343 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 344 |
- embassy-domalign-0.1.0-r3.ebuild: |
| 345 |
- Stabilised on amd64 and x86. |
| 346 |
- |
| 347 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 348 |
- -embassy-domalign-0.1.0-r2.ebuild: |
| 349 |
- Pruning version that will never be stabilised. |
| 350 |
- |
| 351 |
-*embassy-domalign-0.1.0-r3 (27 Aug 2008) |
| 352 |
- |
| 353 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 354 |
- +embassy-domalign-0.1.0-r3.ebuild: |
| 355 |
- New upstream version/package for EMBASSY 6.0.1. |
| 356 |
- |
| 357 |
-*embassy-domalign-0.1.0-r2 (18 Jul 2007) |
| 358 |
- |
| 359 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 360 |
- +embassy-domalign-0.1.0-r2.ebuild: |
| 361 |
- New upstream packaging for EMBOSS 5.0.0. |
| 362 |
- |
| 363 |
- 16 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 364 |
- embassy-domalign-0.1.0-r1.ebuild: |
| 365 |
- Added ~amd64. |
| 366 |
- |
| 367 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 368 |
- -embassy-domalign-0.1.0.ebuild: |
| 369 |
- Pruning old version. |
| 370 |
- |
| 371 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-domalign-0.1.0-r1.ebuild: |
| 372 |
- Stable on ppc wrt bug 153766 |
| 373 |
- |
| 374 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> ChangeLog: |
| 375 |
- Removed hidden file .#embassy-domalign-0.1.0-r1.ebuild.1.2 |
| 376 |
- |
| 377 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> ChangeLog: |
| 378 |
- Added ~sparc |
| 379 |
- |
| 380 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 381 |
- embassy-domalign-0.1.0.ebuild, embassy-domalign-0.1.0-r1.ebuild: |
| 382 |
- Dropped ppc-macos, see you in prefix. |
| 383 |
- |
| 384 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 385 |
- embassy-domalign-0.1.0-r1.ebuild: |
| 386 |
- Added to x86. |
| 387 |
- |
| 388 |
-*embassy-domalign-0.1.0-r1 (21 Jul 2006) |
| 389 |
- |
| 390 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 391 |
- +embassy-domalign-0.1.0-r1.ebuild: |
| 392 |
- New upstream version building against EMBOSS 4.0.0. |
| 393 |
- |
| 394 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 395 |
- embassy-domalign-0.1.0.ebuild: |
| 396 |
- Fixed download URL (silent upstream repackaging). |
| 397 |
- |
| 398 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 399 |
- embassy-domalign-0.1.0.ebuild: |
| 400 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 401 |
- |
| 402 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 403 |
- embassy-domalign-0.1.0.ebuild: |
| 404 |
- Stable on ppc. |
| 405 |
- |
| 406 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 407 |
- embassy-domalign-0.1.0.ebuild: |
| 408 |
- Added to x86. |
| 409 |
- |
| 410 |
-*embassy-domalign-0.1.0 (07 Aug 2005) |
| 411 |
- |
| 412 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 413 |
- +embassy-domalign-0.1.0.ebuild: |
| 414 |
- Initial import. Part of EMBASSY 3.0.0. |
| 415 |
- |
| 416 |
|
| 417 |
diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild |
| 418 |
deleted file mode 100644 |
| 419 |
index 62621f3..0000000 |
| 420 |
--- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild |
| 421 |
+++ /dev/null |
| 422 |
@@ -1,15 +0,0 @@ |
| 423 |
-# Copyright 1999-2015 Gentoo Foundation |
| 424 |
-# Distributed under the terms of the GNU General Public License v2 |
| 425 |
-# $Header: $ |
| 426 |
- |
| 427 |
-EAPI=5 |
| 428 |
- |
| 429 |
-EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment" |
| 430 |
- |
| 431 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 432 |
-AUTOTOOLS_AUTORECONF=1 |
| 433 |
-inherit emboss-r1 |
| 434 |
- |
| 435 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 436 |
- |
| 437 |
-RDEPEND+=" sci-biology/clustal-omega" |
| 438 |
|
| 439 |
diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch |
| 440 |
deleted file mode 100644 |
| 441 |
index 7847da7..0000000 |
| 442 |
--- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch |
| 443 |
+++ /dev/null |
| 444 |
@@ -1,90 +0,0 @@ |
| 445 |
---- CLUSTALOMEGA-1.1.0/configure.ac |
| 446 |
-+++ CLUSTALOMEGA-1.1.0/configure.ac |
| 447 |
-@@ -635,33 +635,6 @@ |
| 448 |
- |
| 449 |
- |
| 450 |
- |
| 451 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 452 |
--dnl to see which version's configure.in these lines come from |
| 453 |
-- |
| 454 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 455 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 456 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 457 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 458 |
--dnl that many releases anyway. |
| 459 |
-- |
| 460 |
--PCRE_MAJOR="7" |
| 461 |
--PCRE_MINOR="9" |
| 462 |
--PCRE_DATE="11-Apr-2009" |
| 463 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 464 |
-- |
| 465 |
--dnl Default values for miscellaneous macros |
| 466 |
-- |
| 467 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 468 |
-- |
| 469 |
--dnl Provide versioning information for libtool shared libraries that |
| 470 |
--dnl are built by default on Unix systems. |
| 471 |
-- |
| 472 |
--PCRE_LIB_VERSION="0:1:0" |
| 473 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 474 |
-- |
| 475 |
-- |
| 476 |
-- |
| 477 |
-- |
| 478 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 479 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 480 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 481 |
-@@ -737,21 +710,6 @@ |
| 482 |
- |
| 483 |
- |
| 484 |
- |
| 485 |
--dnl "Export" these variables for PCRE |
| 486 |
-- |
| 487 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 488 |
--AC_SUBST([HAVE_STRERROR]) |
| 489 |
--AC_SUBST([PCRE_MAJOR]) |
| 490 |
--AC_SUBST([PCRE_MINOR]) |
| 491 |
--AC_SUBST([PCRE_DATE]) |
| 492 |
--AC_SUBST([PCRE_VERSION]) |
| 493 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 494 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 495 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 496 |
-- |
| 497 |
-- |
| 498 |
-- |
| 499 |
-- |
| 500 |
- dnl Test if --enable-localforce given |
| 501 |
- locallink="no" |
| 502 |
- embprefix="/usr/local" |
| 503 |
-@@ -874,6 +832,11 @@ |
| 504 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 505 |
- |
| 506 |
- |
| 507 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 508 |
-+[ |
| 509 |
-+dnl using system libraries |
| 510 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 511 |
-+]) |
| 512 |
- |
| 513 |
- |
| 514 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 515 |
---- CLUSTALOMEGA-1.1.0/src/Makefile.am |
| 516 |
-+++ CLUSTALOMEGA-1.1.0/src/Makefile.am |
| 517 |
-@@ -17,9 +17,7 @@ |
| 518 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 519 |
- -I../../../ajax/acd -I../../../plplot |
| 520 |
- else |
| 521 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 522 |
-- $(NLINCLUDES) \ |
| 523 |
-- -I${embprefix}/include/epcre |
| 524 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 525 |
- endif |
| 526 |
- |
| 527 |
- if ISSHARED |
| 528 |
-@@ -62,5 +60,5 @@ |
| 529 |
- $(XLIB) |
| 530 |
- else |
| 531 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 532 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 533 |
-+ -lajax $(NLADD) $(XLIB) |
| 534 |
- endif |
| 535 |
|
| 536 |
diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml |
| 537 |
deleted file mode 100644 |
| 538 |
index f17a827..0000000 |
| 539 |
--- a/sci-biology/embassy-clustalomega/metadata.xml |
| 540 |
+++ /dev/null |
| 541 |
@@ -1,5 +0,0 @@ |
| 542 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 543 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 544 |
-<pkgmetadata> |
| 545 |
- <herd>sci-biology</herd> |
| 546 |
-</pkgmetadata> |
| 547 |
|
| 548 |
diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog |
| 549 |
deleted file mode 100644 |
| 550 |
index e55b3b7..0000000 |
| 551 |
--- a/sci-biology/embassy-domainatrix/ChangeLog |
| 552 |
+++ /dev/null |
| 553 |
@@ -1,174 +0,0 @@ |
| 554 |
-# ChangeLog for sci-biology/embassy-domainatrix |
| 555 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 556 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.29 2010/01/01 21:48:13 fauli Exp $ |
| 557 |
- |
| 558 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 559 |
- -embassy-domainatrix-0.1.0-r6.ebuild, embassy-domainatrix-0.1.650.ebuild, |
| 560 |
- -files/embassy-domainatrix-0.1.0-r5.patch, metadata.xml: |
| 561 |
- Bump eclass, Drop old |
| 562 |
- |
| 563 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 564 |
- embassy-domainatrix-0.1.0-r5.ebuild: |
| 565 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 566 |
- |
| 567 |
- 19 Mar 2011; Justin Lecher <jlec@g.o> |
| 568 |
- embassy-domainatrix-0.1.0-r5.ebuild, |
| 569 |
- files/embassy-domainatrix-0.1.0-r5.patch: |
| 570 |
- Fixed for reviewed eclass |
| 571 |
- |
| 572 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 573 |
- embassy-domainatrix-0.1.0-r5.ebuild: |
| 574 |
- Naming of eclass changed |
| 575 |
- |
| 576 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 577 |
- embassy-domainatrix-0.1.0-r5.ebuild: |
| 578 |
- EOV not needed to be set anymore |
| 579 |
- |
| 580 |
-*embassy-domainatrix-0.1.0-r5 (10 Mar 2011) |
| 581 |
- |
| 582 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 583 |
- +embassy-domainatrix-0.1.0-r5.ebuild, |
| 584 |
- +files/embassy-domainatrix-0.1.0-r5.patch, +metadata.xml: |
| 585 |
- Move to new embassy-ng.eclass |
| 586 |
- |
| 587 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 588 |
- embassy-domainatrix-0.1.0-r4.ebuild: |
| 589 |
- Transfer Prefix keywords |
| 590 |
- |
| 591 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 592 |
- Giving up maintainership of this package. |
| 593 |
- |
| 594 |
-*embassy-domainatrix-0.1.0-r4 (01 Sep 2009) |
| 595 |
- |
| 596 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 597 |
- +embassy-domainatrix-0.1.0-r4.ebuild: |
| 598 |
- Updated version for EMBASSY 6.1.0. |
| 599 |
- |
| 600 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 601 |
- embassy-domainatrix-0.1.0-r3.ebuild: |
| 602 |
- Stabilised on amd64 and x86. |
| 603 |
- |
| 604 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 605 |
- -embassy-domainatrix-0.1.0-r2.ebuild: |
| 606 |
- Pruning version that will never be stabilised. |
| 607 |
- |
| 608 |
-*embassy-domainatrix-0.1.0-r3 (27 Aug 2008) |
| 609 |
- |
| 610 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 611 |
- +embassy-domainatrix-0.1.0-r3.ebuild: |
| 612 |
- New upstream version/package for EMBASSY 6.0.1. |
| 613 |
- |
| 614 |
-*embassy-domainatrix-0.1.0-r2 (18 Jul 2007) |
| 615 |
- |
| 616 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 617 |
- +embassy-domainatrix-0.1.0-r2.ebuild: |
| 618 |
- New upstream packaging for EMBOSS 5.0.0. |
| 619 |
- |
| 620 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 621 |
- embassy-domainatrix-0.1.0-r1.ebuild: |
| 622 |
- Added ~amd64. |
| 623 |
- |
| 624 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 625 |
- -embassy-domainatrix-0.1.0.ebuild: |
| 626 |
- Pruning old version. |
| 627 |
- |
| 628 |
- 03 Nov 2006; nixnut <nixnut@g.o> |
| 629 |
- embassy-domainatrix-0.1.0-r1.ebuild: |
| 630 |
- Stable on ppc wrt bug 153766 |
| 631 |
- |
| 632 |
- 03 Nov 2006; Fabian Groffen <grobian@g.o> |
| 633 |
- embassy-domainatrix-0.1.0.ebuild, embassy-domainatrix-0.1.0-r1.ebuild: |
| 634 |
- Dropped ppc-macos, see you in prefix. |
| 635 |
- |
| 636 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 637 |
- embassy-domainatrix-0.1.0-r1.ebuild: |
| 638 |
- Added ~sparc |
| 639 |
- |
| 640 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 641 |
- embassy-domainatrix-0.1.0-r1.ebuild: |
| 642 |
- Added to x86. |
| 643 |
- |
| 644 |
-*embassy-domainatrix-0.1.0-r1 (21 Jul 2006) |
| 645 |
- |
| 646 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 647 |
- +embassy-domainatrix-0.1.0-r1.ebuild: |
| 648 |
- New upstream version building against EMBOSS 4.0.0. |
| 649 |
- |
| 650 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 651 |
- embassy-domainatrix-0.1.0.ebuild: |
| 652 |
- Fixed download URL (silent upstream repackaging). |
| 653 |
- |
| 654 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 655 |
- -files/embassy-domainatrix-1.0.0-r1.patch, |
| 656 |
- -embassy-domainatrix-1.0.0-r1.ebuild: |
| 657 |
- Removed obsolete version. |
| 658 |
- |
| 659 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 660 |
- embassy-domainatrix-0.1.0.ebuild: |
| 661 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 662 |
- |
| 663 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 664 |
- embassy-domainatrix-0.1.0.ebuild: |
| 665 |
- Stable on ppc. |
| 666 |
- |
| 667 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 668 |
- embassy-domainatrix-0.1.0.ebuild: |
| 669 |
- Added to x86. |
| 670 |
- |
| 671 |
-*embassy-domainatrix-0.1.0 (07 Aug 2005) |
| 672 |
- |
| 673 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> |
| 674 |
- +embassy-domainatrix-0.1.0.ebuild, embassy-domainatrix-1.0.0-r1.ebuild: |
| 675 |
- Ported version 1.0.0-r1 to the improved embassy.eclass. Version 0.1.0 is |
| 676 |
- really an upgrade; it is normal to be required to downgrade from 1.0.0 to |
| 677 |
- 0.1.0 to upgrade to EMBASSY 3.0.0. This is an issue with upstream's |
| 678 |
- versionning scheme. |
| 679 |
- |
| 680 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 681 |
- -embassy-domainatrix-1.0.0.ebuild: |
| 682 |
- Removed old version. |
| 683 |
- |
| 684 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> |
| 685 |
- embassy-domainatrix-1.0.0-r1.ebuild: |
| 686 |
- Stable ppc-macos |
| 687 |
- |
| 688 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> |
| 689 |
- embassy-domainatrix-1.0.0-r1.ebuild: |
| 690 |
- Marked ppc stable. |
| 691 |
- |
| 692 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> |
| 693 |
- embassy-domainatrix-1.0.0-r1.ebuild: |
| 694 |
- Added to x86. |
| 695 |
- |
| 696 |
-*embassy-domainatrix-1.0.0-r1 (25 Mar 2005) |
| 697 |
- |
| 698 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> |
| 699 |
- +files/embassy-domainatrix-1.0.0-r1.patch, |
| 700 |
- +embassy-domainatrix-1.0.0-r1.ebuild: |
| 701 |
- Patched version for EMBOSS-2.10. |
| 702 |
- |
| 703 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> |
| 704 |
- embassy-domainatrix-1.0.0.ebuild: |
| 705 |
- Stable ppc-macos |
| 706 |
- |
| 707 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-domainatrix-1.0.0.ebuild: |
| 708 |
- Unstable ppc-macos. |
| 709 |
- |
| 710 |
-*embassy-domainatrix-1.0.0 (23 Dec 2004) |
| 711 |
- |
| 712 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 713 |
- +embassy-domainatrix-1.0.0.ebuild: |
| 714 |
- Moved from app-sci/embassy-domainatrix to sci-biology/embassy-domainatrix. |
| 715 |
- |
| 716 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> |
| 717 |
- embassy-domainatrix-1.0.0.ebuild: |
| 718 |
- Added to x86. |
| 719 |
- |
| 720 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-domainatrix-1.0.0.ebuild: |
| 721 |
- Added to ~ppc. |
| 722 |
- |
| 723 |
-* domainatrix-1.0.0 (19 Jul 2004) |
| 724 |
- |
| 725 |
- 14 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 726 |
- embassy-domainatrix-1.0.0.ebuild, metadata.xml, ChangeLog |
| 727 |
- Initial import. |
| 728 |
|
| 729 |
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild |
| 730 |
deleted file mode 100644 |
| 731 |
index 276f646..0000000 |
| 732 |
--- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild |
| 733 |
+++ /dev/null |
| 734 |
@@ -1,13 +0,0 @@ |
| 735 |
-# Copyright 1999-2015 Gentoo Foundation |
| 736 |
-# Distributed under the terms of the GNU General Public License v2 |
| 737 |
-# $Header: $ |
| 738 |
- |
| 739 |
-EAPI=5 |
| 740 |
- |
| 741 |
-EBO_DESCRIPTION="Protein domain analysis add-on package" |
| 742 |
- |
| 743 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 744 |
-AUTOTOOLS_AUTORECONF=1 |
| 745 |
-inherit emboss-r1 |
| 746 |
- |
| 747 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 748 |
|
| 749 |
diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch |
| 750 |
deleted file mode 100644 |
| 751 |
index f76b023..0000000 |
| 752 |
--- a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch |
| 753 |
+++ /dev/null |
| 754 |
@@ -1,91 +0,0 @@ |
| 755 |
---- DOMAINATRIX-0.1.650/configure.ac |
| 756 |
-+++ DOMAINATRIX-0.1.650/configure.ac |
| 757 |
-@@ -635,33 +635,6 @@ |
| 758 |
- |
| 759 |
- |
| 760 |
- |
| 761 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 762 |
--dnl to see which version's configure.in these lines come from |
| 763 |
-- |
| 764 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 765 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 766 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 767 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 768 |
--dnl that many releases anyway. |
| 769 |
-- |
| 770 |
--PCRE_MAJOR="7" |
| 771 |
--PCRE_MINOR="9" |
| 772 |
--PCRE_DATE="11-Apr-2009" |
| 773 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 774 |
-- |
| 775 |
--dnl Default values for miscellaneous macros |
| 776 |
-- |
| 777 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 778 |
-- |
| 779 |
--dnl Provide versioning information for libtool shared libraries that |
| 780 |
--dnl are built by default on Unix systems. |
| 781 |
-- |
| 782 |
--PCRE_LIB_VERSION="0:1:0" |
| 783 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 784 |
-- |
| 785 |
-- |
| 786 |
-- |
| 787 |
-- |
| 788 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 789 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 790 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 791 |
-@@ -737,21 +710,6 @@ |
| 792 |
- |
| 793 |
- |
| 794 |
- |
| 795 |
--dnl "Export" these variables for PCRE |
| 796 |
-- |
| 797 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 798 |
--AC_SUBST([HAVE_STRERROR]) |
| 799 |
--AC_SUBST([PCRE_MAJOR]) |
| 800 |
--AC_SUBST([PCRE_MINOR]) |
| 801 |
--AC_SUBST([PCRE_DATE]) |
| 802 |
--AC_SUBST([PCRE_VERSION]) |
| 803 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 804 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 805 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 806 |
-- |
| 807 |
-- |
| 808 |
-- |
| 809 |
-- |
| 810 |
- dnl Test if --enable-localforce given |
| 811 |
- locallink="no" |
| 812 |
- embprefix="/usr/local" |
| 813 |
-@@ -874,6 +832,11 @@ |
| 814 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 815 |
- |
| 816 |
- |
| 817 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 818 |
-+[ |
| 819 |
-+dnl using system libraries |
| 820 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 821 |
-+]) |
| 822 |
- |
| 823 |
- |
| 824 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 825 |
---- DOMAINATRIX-0.1.650/src/Makefile.am |
| 826 |
-+++ DOMAINATRIX-0.1.650/src/Makefile.am |
| 827 |
-@@ -17,9 +17,7 @@ |
| 828 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 829 |
- -I../../../ajax/acd -I../../../plplot |
| 830 |
- else |
| 831 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 832 |
-- $(NLINCLUDES) \ |
| 833 |
-- -I${embprefix}/include/epcre |
| 834 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 835 |
- endif |
| 836 |
- |
| 837 |
- if ISSHARED |
| 838 |
-@@ -64,5 +62,5 @@ |
| 839 |
- $(XLIB) |
| 840 |
- else |
| 841 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 842 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 843 |
-+ -lajax $(NLADD) $(XLIB) |
| 844 |
- endif |
| 845 |
- |
| 846 |
|
| 847 |
diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml |
| 848 |
deleted file mode 100644 |
| 849 |
index f17a827..0000000 |
| 850 |
--- a/sci-biology/embassy-domainatrix/metadata.xml |
| 851 |
+++ /dev/null |
| 852 |
@@ -1,5 +0,0 @@ |
| 853 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 854 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 855 |
-<pkgmetadata> |
| 856 |
- <herd>sci-biology</herd> |
| 857 |
-</pkgmetadata> |
| 858 |
|
| 859 |
diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog |
| 860 |
deleted file mode 100644 |
| 861 |
index 35ad6db..0000000 |
| 862 |
--- a/sci-biology/embassy-domalign/ChangeLog |
| 863 |
+++ /dev/null |
| 864 |
@@ -1,118 +0,0 @@ |
| 865 |
-# ChangeLog for sci-biology/embassy-domalign |
| 866 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 867 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.20 2010/01/01 21:51:36 fauli Exp $ |
| 868 |
- |
| 869 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 870 |
- -embassy-domalign-0.1.0-r5.ebuild, embassy-domalign-0.1.650.ebuild, |
| 871 |
- -files/embassy-domalign-0.1.0-r5.patch, metadata.xml: |
| 872 |
- Bump eclass, Drop old |
| 873 |
- |
| 874 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 875 |
- embassy-domalign-0.1.0-r5.ebuild: |
| 876 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 877 |
- |
| 878 |
- 19 Mar 2011; Justin Lecher <jlec@g.o> |
| 879 |
- embassy-domalign-0.1.0-r5.ebuild, files/embassy-domalign-0.1.0-r5.patch: |
| 880 |
- Fixed for reviewed eclass |
| 881 |
- |
| 882 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 883 |
- embassy-domalign-0.1.0-r5.ebuild: |
| 884 |
- Naming of eclass changed |
| 885 |
- |
| 886 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 887 |
- embassy-domalign-0.1.0-r5.ebuild: |
| 888 |
- EOV not needed to be set anymore |
| 889 |
- |
| 890 |
-*embassy-domalign-0.1.0-r5 (10 Mar 2011) |
| 891 |
- |
| 892 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 893 |
- +embassy-domalign-0.1.0-r5.ebuild, +files/embassy-domalign-0.1.0-r5.patch, |
| 894 |
- +metadata.xml: |
| 895 |
- Move to new embassy-ng.eclass |
| 896 |
- |
| 897 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 898 |
- embassy-domalign-0.1.0-r4.ebuild: |
| 899 |
- Transfer Prefix keywords |
| 900 |
- |
| 901 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 902 |
- Giving up maintainership of this package. |
| 903 |
- |
| 904 |
-*embassy-domalign-0.1.0-r4 (01 Sep 2009) |
| 905 |
- |
| 906 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 907 |
- +embassy-domalign-0.1.0-r4.ebuild: |
| 908 |
- Updated version for EMBASSY 6.1.0. |
| 909 |
- |
| 910 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 911 |
- embassy-domalign-0.1.0-r3.ebuild: |
| 912 |
- Stabilised on amd64 and x86. |
| 913 |
- |
| 914 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 915 |
- -embassy-domalign-0.1.0-r2.ebuild: |
| 916 |
- Pruning version that will never be stabilised. |
| 917 |
- |
| 918 |
-*embassy-domalign-0.1.0-r3 (27 Aug 2008) |
| 919 |
- |
| 920 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 921 |
- +embassy-domalign-0.1.0-r3.ebuild: |
| 922 |
- New upstream version/package for EMBASSY 6.0.1. |
| 923 |
- |
| 924 |
-*embassy-domalign-0.1.0-r2 (18 Jul 2007) |
| 925 |
- |
| 926 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 927 |
- +embassy-domalign-0.1.0-r2.ebuild: |
| 928 |
- New upstream packaging for EMBOSS 5.0.0. |
| 929 |
- |
| 930 |
- 16 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 931 |
- embassy-domalign-0.1.0-r1.ebuild: |
| 932 |
- Added ~amd64. |
| 933 |
- |
| 934 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 935 |
- -embassy-domalign-0.1.0.ebuild: |
| 936 |
- Pruning old version. |
| 937 |
- |
| 938 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-domalign-0.1.0-r1.ebuild: |
| 939 |
- Stable on ppc wrt bug 153766 |
| 940 |
- |
| 941 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> ChangeLog: |
| 942 |
- Removed hidden file .#embassy-domalign-0.1.0-r1.ebuild.1.2 |
| 943 |
- |
| 944 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> ChangeLog: |
| 945 |
- Added ~sparc |
| 946 |
- |
| 947 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 948 |
- embassy-domalign-0.1.0.ebuild, embassy-domalign-0.1.0-r1.ebuild: |
| 949 |
- Dropped ppc-macos, see you in prefix. |
| 950 |
- |
| 951 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 952 |
- embassy-domalign-0.1.0-r1.ebuild: |
| 953 |
- Added to x86. |
| 954 |
- |
| 955 |
-*embassy-domalign-0.1.0-r1 (21 Jul 2006) |
| 956 |
- |
| 957 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 958 |
- +embassy-domalign-0.1.0-r1.ebuild: |
| 959 |
- New upstream version building against EMBOSS 4.0.0. |
| 960 |
- |
| 961 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 962 |
- embassy-domalign-0.1.0.ebuild: |
| 963 |
- Fixed download URL (silent upstream repackaging). |
| 964 |
- |
| 965 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 966 |
- embassy-domalign-0.1.0.ebuild: |
| 967 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 968 |
- |
| 969 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 970 |
- embassy-domalign-0.1.0.ebuild: |
| 971 |
- Stable on ppc. |
| 972 |
- |
| 973 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 974 |
- embassy-domalign-0.1.0.ebuild: |
| 975 |
- Added to x86. |
| 976 |
- |
| 977 |
-*embassy-domalign-0.1.0 (07 Aug 2005) |
| 978 |
- |
| 979 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 980 |
- +embassy-domalign-0.1.0.ebuild: |
| 981 |
- Initial import. Part of EMBASSY 3.0.0. |
| 982 |
- |
| 983 |
|
| 984 |
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild |
| 985 |
deleted file mode 100644 |
| 986 |
index 140ab99..0000000 |
| 987 |
--- a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild |
| 988 |
+++ /dev/null |
| 989 |
@@ -1,13 +0,0 @@ |
| 990 |
-# Copyright 1999-2015 Gentoo Foundation |
| 991 |
-# Distributed under the terms of the GNU General Public License v2 |
| 992 |
-# $Header: $ |
| 993 |
- |
| 994 |
-EAPI=5 |
| 995 |
- |
| 996 |
-EBO_DESCRIPTION="Protein domain alignment add-on package" |
| 997 |
- |
| 998 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 999 |
-AUTOTOOLS_AUTORECONF=1 |
| 1000 |
-inherit emboss-r1 |
| 1001 |
- |
| 1002 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 1003 |
|
| 1004 |
diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch |
| 1005 |
deleted file mode 100644 |
| 1006 |
index d87bae3..0000000 |
| 1007 |
--- a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch |
| 1008 |
+++ /dev/null |
| 1009 |
@@ -1,92 +0,0 @@ |
| 1010 |
---- DOMALIGN-0.1.650/configure.ac |
| 1011 |
-+++ DOMALIGN-0.1.650/configure.ac |
| 1012 |
-@@ -635,33 +635,6 @@ |
| 1013 |
- |
| 1014 |
- |
| 1015 |
- |
| 1016 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 1017 |
--dnl to see which version's configure.in these lines come from |
| 1018 |
-- |
| 1019 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 1020 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 1021 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 1022 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 1023 |
--dnl that many releases anyway. |
| 1024 |
-- |
| 1025 |
--PCRE_MAJOR="7" |
| 1026 |
--PCRE_MINOR="9" |
| 1027 |
--PCRE_DATE="11-Apr-2009" |
| 1028 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 1029 |
-- |
| 1030 |
--dnl Default values for miscellaneous macros |
| 1031 |
-- |
| 1032 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 1033 |
-- |
| 1034 |
--dnl Provide versioning information for libtool shared libraries that |
| 1035 |
--dnl are built by default on Unix systems. |
| 1036 |
-- |
| 1037 |
--PCRE_LIB_VERSION="0:1:0" |
| 1038 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 1039 |
-- |
| 1040 |
-- |
| 1041 |
-- |
| 1042 |
-- |
| 1043 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 1044 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 1045 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 1046 |
-@@ -737,21 +710,6 @@ |
| 1047 |
- |
| 1048 |
- |
| 1049 |
- |
| 1050 |
--dnl "Export" these variables for PCRE |
| 1051 |
-- |
| 1052 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 1053 |
--AC_SUBST([HAVE_STRERROR]) |
| 1054 |
--AC_SUBST([PCRE_MAJOR]) |
| 1055 |
--AC_SUBST([PCRE_MINOR]) |
| 1056 |
--AC_SUBST([PCRE_DATE]) |
| 1057 |
--AC_SUBST([PCRE_VERSION]) |
| 1058 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 1059 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 1060 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 1061 |
-- |
| 1062 |
-- |
| 1063 |
-- |
| 1064 |
-- |
| 1065 |
- dnl Test if --enable-localforce given |
| 1066 |
- locallink="no" |
| 1067 |
- embprefix="/usr/local" |
| 1068 |
-@@ -874,6 +832,11 @@ |
| 1069 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 1070 |
- |
| 1071 |
- |
| 1072 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 1073 |
-+[ |
| 1074 |
-+dnl using system libraries |
| 1075 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 1076 |
-+]) |
| 1077 |
- |
| 1078 |
- |
| 1079 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 1080 |
---- DOMALIGN-0.1.650/src/Makefile.am |
| 1081 |
-+++ DOMALIGN-0.1.650/src/Makefile.am |
| 1082 |
-@@ -17,10 +17,7 @@ |
| 1083 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 1084 |
- -I../../../ajax/acd -I../../../plplot |
| 1085 |
- else |
| 1086 |
--AM_CPPFLAGS = -I../include -I${embprefix}/include \ |
| 1087 |
-- -I${embprefix}/include/eplplot \ |
| 1088 |
-- $(NLINCLUDES) \ |
| 1089 |
-- -I${embprefix}/include/epcre |
| 1090 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 1091 |
- endif |
| 1092 |
- |
| 1093 |
- if ISSHARED |
| 1094 |
-@@ -63,5 +60,5 @@ |
| 1095 |
- ../../../plplot/libeplplot.la $(XLIB) |
| 1096 |
- else |
| 1097 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 1098 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 1099 |
-+ -lajax $(NLADD) $(XLIB) |
| 1100 |
- endif |
| 1101 |
- |
| 1102 |
|
| 1103 |
diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml |
| 1104 |
deleted file mode 100644 |
| 1105 |
index f17a827..0000000 |
| 1106 |
--- a/sci-biology/embassy-domalign/metadata.xml |
| 1107 |
+++ /dev/null |
| 1108 |
@@ -1,5 +0,0 @@ |
| 1109 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 1110 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 1111 |
-<pkgmetadata> |
| 1112 |
- <herd>sci-biology</herd> |
| 1113 |
-</pkgmetadata> |
| 1114 |
|
| 1115 |
diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog |
| 1116 |
deleted file mode 100644 |
| 1117 |
index db2a175..0000000 |
| 1118 |
--- a/sci-biology/embassy-domsearch/ChangeLog |
| 1119 |
+++ /dev/null |
| 1120 |
@@ -1,116 +0,0 @@ |
| 1121 |
-# ChangeLog for sci-biology/embassy-domsearch |
| 1122 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 1123 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.19 2010/01/01 21:53:24 fauli Exp $ |
| 1124 |
- |
| 1125 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 1126 |
- -embassy-domsearch-0.1.0-r5.ebuild, embassy-domsearch-0.1.650.ebuild, |
| 1127 |
- -files/embassy-domsearch-0.1.0-r5.patch, metadata.xml: |
| 1128 |
- Bump eclass, Drop old |
| 1129 |
- |
| 1130 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 1131 |
- embassy-domsearch-0.1.0-r5.ebuild: |
| 1132 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 1133 |
- |
| 1134 |
- 19 Mar 2011; Justin Lecher <jlec@g.o> |
| 1135 |
- embassy-domsearch-0.1.0-r5.ebuild, files/embassy-domsearch-0.1.0-r5.patch: |
| 1136 |
- Fixed for reviewed eclass |
| 1137 |
- |
| 1138 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 1139 |
- embassy-domsearch-0.1.0-r5.ebuild: |
| 1140 |
- Naming of eclass changed |
| 1141 |
- |
| 1142 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 1143 |
- embassy-domsearch-0.1.0-r5.ebuild: |
| 1144 |
- EOV not needed to be set anymore |
| 1145 |
- |
| 1146 |
-*embassy-domsearch-0.1.0-r5 (10 Mar 2011) |
| 1147 |
- |
| 1148 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 1149 |
- +embassy-domsearch-0.1.0-r5.ebuild, +files/embassy-domsearch-0.1.0-r5.patch, |
| 1150 |
- +metadata.xml: |
| 1151 |
- Move to new embassy-ng.eclass |
| 1152 |
- |
| 1153 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 1154 |
- embassy-domsearch-0.1.0-r4.ebuild: |
| 1155 |
- Transfer Prefix keywords |
| 1156 |
- |
| 1157 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 1158 |
- Giving up maintainership of this package. |
| 1159 |
- |
| 1160 |
-*embassy-domsearch-0.1.0-r4 (01 Sep 2009) |
| 1161 |
- |
| 1162 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 1163 |
- +embassy-domsearch-0.1.0-r4.ebuild: |
| 1164 |
- Updated version for EMBASSY 6.1.0. |
| 1165 |
- |
| 1166 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 1167 |
- embassy-domsearch-0.1.0-r3.ebuild: |
| 1168 |
- Stabilised on amd64 and x86. |
| 1169 |
- |
| 1170 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 1171 |
- -embassy-domsearch-0.1.0-r2.ebuild: |
| 1172 |
- Pruning version that will never be stabilised. |
| 1173 |
- |
| 1174 |
-*embassy-domsearch-0.1.0-r3 (27 Aug 2008) |
| 1175 |
- |
| 1176 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 1177 |
- +embassy-domsearch-0.1.0-r3.ebuild: |
| 1178 |
- New upstream version/package for EMBASSY 6.0.1. |
| 1179 |
- |
| 1180 |
-*embassy-domsearch-0.1.0-r2 (18 Jul 2007) |
| 1181 |
- |
| 1182 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 1183 |
- +embassy-domsearch-0.1.0-r2.ebuild: |
| 1184 |
- New upstream packaging for EMBOSS 5.0.0. |
| 1185 |
- |
| 1186 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 1187 |
- embassy-domsearch-0.1.0-r1.ebuild: |
| 1188 |
- Added ~amd64. |
| 1189 |
- |
| 1190 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 1191 |
- -embassy-domsearch-0.1.0.ebuild: |
| 1192 |
- Pruning old version. |
| 1193 |
- |
| 1194 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-domsearch-0.1.0-r1.ebuild: |
| 1195 |
- Stable on ppc wrt bug 153766 |
| 1196 |
- |
| 1197 |
- 03 Nov 2006; Fabian Groffen <grobian@g.o> |
| 1198 |
- embassy-domsearch-0.1.0.ebuild, embassy-domsearch-0.1.0-r1.ebuild: |
| 1199 |
- Dropped ppc-macos, see you in prefix. |
| 1200 |
- |
| 1201 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 1202 |
- embassy-domsearch-0.1.0-r1.ebuild: |
| 1203 |
- Added ~sparc |
| 1204 |
- |
| 1205 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 1206 |
- embassy-domsearch-0.1.0-r1.ebuild: |
| 1207 |
- Added to x86. |
| 1208 |
- |
| 1209 |
-*embassy-domsearch-0.1.0-r1 (21 Jul 2006) |
| 1210 |
- |
| 1211 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 1212 |
- +embassy-domsearch-0.1.0-r1.ebuild: |
| 1213 |
- New upstream version building against EMBOSS 4.0.0. |
| 1214 |
- |
| 1215 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 1216 |
- embassy-domsearch-0.1.0.ebuild: |
| 1217 |
- Fixed download URL (silent upstream repackaging). |
| 1218 |
- |
| 1219 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 1220 |
- embassy-domsearch-0.1.0.ebuild: |
| 1221 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 1222 |
- |
| 1223 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 1224 |
- embassy-domsearch-0.1.0.ebuild: |
| 1225 |
- Stable on ppc. |
| 1226 |
- |
| 1227 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 1228 |
- embassy-domsearch-0.1.0.ebuild: |
| 1229 |
- Added to x86. |
| 1230 |
- |
| 1231 |
-*embassy-domsearch-0.1.0 (07 Aug 2005) |
| 1232 |
- |
| 1233 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 1234 |
- +embassy-domsearch-0.1.0.ebuild: |
| 1235 |
- Initial import. Part of EMBASSY 3.0.0. |
| 1236 |
- |
| 1237 |
|
| 1238 |
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild |
| 1239 |
deleted file mode 100644 |
| 1240 |
index 1e1c29c..0000000 |
| 1241 |
--- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild |
| 1242 |
+++ /dev/null |
| 1243 |
@@ -1,13 +0,0 @@ |
| 1244 |
-# Copyright 1999-2015 Gentoo Foundation |
| 1245 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1246 |
-# $Header: $ |
| 1247 |
- |
| 1248 |
-EAPI=5 |
| 1249 |
- |
| 1250 |
-EBO_DESCRIPTION="Protein domain search add-on package" |
| 1251 |
- |
| 1252 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 1253 |
-AUTOTOOLS_AUTORECONF=1 |
| 1254 |
-inherit emboss-r1 |
| 1255 |
- |
| 1256 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 1257 |
|
| 1258 |
diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch |
| 1259 |
deleted file mode 100644 |
| 1260 |
index f3f4b39..0000000 |
| 1261 |
--- a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch |
| 1262 |
+++ /dev/null |
| 1263 |
@@ -1,91 +0,0 @@ |
| 1264 |
---- DOMSEARCH-0.1.650/configure.ac |
| 1265 |
-+++ DOMSEARCH-0.1.650/configure.ac |
| 1266 |
-@@ -635,33 +635,6 @@ |
| 1267 |
- |
| 1268 |
- |
| 1269 |
- |
| 1270 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 1271 |
--dnl to see which version's configure.in these lines come from |
| 1272 |
-- |
| 1273 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 1274 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 1275 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 1276 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 1277 |
--dnl that many releases anyway. |
| 1278 |
-- |
| 1279 |
--PCRE_MAJOR="7" |
| 1280 |
--PCRE_MINOR="9" |
| 1281 |
--PCRE_DATE="11-Apr-2009" |
| 1282 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 1283 |
-- |
| 1284 |
--dnl Default values for miscellaneous macros |
| 1285 |
-- |
| 1286 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 1287 |
-- |
| 1288 |
--dnl Provide versioning information for libtool shared libraries that |
| 1289 |
--dnl are built by default on Unix systems. |
| 1290 |
-- |
| 1291 |
--PCRE_LIB_VERSION="0:1:0" |
| 1292 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 1293 |
-- |
| 1294 |
-- |
| 1295 |
-- |
| 1296 |
-- |
| 1297 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 1298 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 1299 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 1300 |
-@@ -737,21 +710,6 @@ |
| 1301 |
- |
| 1302 |
- |
| 1303 |
- |
| 1304 |
--dnl "Export" these variables for PCRE |
| 1305 |
-- |
| 1306 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 1307 |
--AC_SUBST([HAVE_STRERROR]) |
| 1308 |
--AC_SUBST([PCRE_MAJOR]) |
| 1309 |
--AC_SUBST([PCRE_MINOR]) |
| 1310 |
--AC_SUBST([PCRE_DATE]) |
| 1311 |
--AC_SUBST([PCRE_VERSION]) |
| 1312 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 1313 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 1314 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 1315 |
-- |
| 1316 |
-- |
| 1317 |
-- |
| 1318 |
-- |
| 1319 |
- dnl Test if --enable-localforce given |
| 1320 |
- locallink="no" |
| 1321 |
- embprefix="/usr/local" |
| 1322 |
-@@ -874,6 +832,11 @@ |
| 1323 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 1324 |
- |
| 1325 |
- |
| 1326 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 1327 |
-+[ |
| 1328 |
-+dnl using system libraries |
| 1329 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 1330 |
-+]) |
| 1331 |
- |
| 1332 |
- |
| 1333 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 1334 |
---- DOMSEARCH-0.1.650/src/Makefile.am |
| 1335 |
-+++ DOMSEARCH-0.1.650/src/Makefile.am |
| 1336 |
-@@ -17,9 +17,7 @@ |
| 1337 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 1338 |
- -I../../../ajax/acd -I../../../plplot |
| 1339 |
- else |
| 1340 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 1341 |
-- $(NLINCLUDES) \ |
| 1342 |
-- -I${embprefix}/include/epcre |
| 1343 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 1344 |
- endif |
| 1345 |
- |
| 1346 |
- if ISSHARED |
| 1347 |
-@@ -62,5 +60,5 @@ |
| 1348 |
- ../../../plplot/libeplplot.la $(XLIB) |
| 1349 |
- else |
| 1350 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 1351 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 1352 |
-+ -lajax $(NLADD) $(XLIB) |
| 1353 |
- endif |
| 1354 |
- |
| 1355 |
|
| 1356 |
diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml |
| 1357 |
deleted file mode 100644 |
| 1358 |
index f17a827..0000000 |
| 1359 |
--- a/sci-biology/embassy-domsearch/metadata.xml |
| 1360 |
+++ /dev/null |
| 1361 |
@@ -1,5 +0,0 @@ |
| 1362 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 1363 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 1364 |
-<pkgmetadata> |
| 1365 |
- <herd>sci-biology</herd> |
| 1366 |
-</pkgmetadata> |
| 1367 |
|
| 1368 |
diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog |
| 1369 |
deleted file mode 100644 |
| 1370 |
index a497db7..0000000 |
| 1371 |
--- a/sci-biology/embassy-emnu/ChangeLog |
| 1372 |
+++ /dev/null |
| 1373 |
@@ -1,157 +0,0 @@ |
| 1374 |
-# ChangeLog for sci-biology/embassy-emnu |
| 1375 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 1376 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.29 2010/01/01 21:55:20 fauli Exp $ |
| 1377 |
- |
| 1378 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-emnu-1.05-r7.ebuild, |
| 1379 |
- embassy-emnu-1.05.650.ebuild, -files/embassy-emnu-1.05-r7.patch, |
| 1380 |
- metadata.xml: |
| 1381 |
- Bump eclass, Drop old |
| 1382 |
- |
| 1383 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-emnu-1.05-r7.ebuild: |
| 1384 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 1385 |
- |
| 1386 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-emnu-1.05-r7.ebuild, |
| 1387 |
- files/embassy-emnu-1.05-r7.patch: |
| 1388 |
- Fixed for reviewed eclass |
| 1389 |
- |
| 1390 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-emnu-1.05-r7.ebuild: |
| 1391 |
- Naming of eclass changed |
| 1392 |
- |
| 1393 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-emnu-1.05-r7.ebuild: |
| 1394 |
- EOV not needed to be set anymore |
| 1395 |
- |
| 1396 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 1397 |
- -files/embassy-emnu-1.05-r6.patch, +files/embassy-emnu-1.05-r7.patch: |
| 1398 |
- Move to new embassy-ng.eclass |
| 1399 |
- |
| 1400 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 1401 |
- embassy-emnu-1.05-r6.ebuild: |
| 1402 |
- Transfer Prefix keywords |
| 1403 |
- |
| 1404 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 1405 |
- Giving up maintainership of this package. |
| 1406 |
- |
| 1407 |
-*embassy-emnu-1.05-r6 (01 Sep 2009) |
| 1408 |
- |
| 1409 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 1410 |
- +embassy-emnu-1.05-r6.ebuild: |
| 1411 |
- Updated version for EMBASSY 6.1.0. |
| 1412 |
- |
| 1413 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 1414 |
- embassy-emnu-1.05-r5.ebuild: |
| 1415 |
- Stabilised on amd64 and x86. |
| 1416 |
- |
| 1417 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 1418 |
- -embassy-emnu-1.05-r4.ebuild: |
| 1419 |
- Pruning version that will never be stabilised. |
| 1420 |
- |
| 1421 |
-*embassy-emnu-1.05-r5 (27 Aug 2008) |
| 1422 |
- |
| 1423 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 1424 |
- +embassy-emnu-1.05-r5.ebuild: |
| 1425 |
- New upstream version/package for EMBASSY 6.0.1. |
| 1426 |
- |
| 1427 |
-*embassy-emnu-1.05-r4 (18 Jul 2007) |
| 1428 |
- |
| 1429 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 1430 |
- +embassy-emnu-1.05-r4.ebuild: |
| 1431 |
- New upstream packaging for EMBOSS 5.0.0. |
| 1432 |
- |
| 1433 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> embassy-emnu-1.05-r3.ebuild: |
| 1434 |
- Added ~amd64. |
| 1435 |
- |
| 1436 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 1437 |
- -embassy-emnu-1.05-r2.ebuild: |
| 1438 |
- Pruning old version. |
| 1439 |
- |
| 1440 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-emnu-1.05-r3.ebuild: |
| 1441 |
- Stable on ppc wrt bug 153766 |
| 1442 |
- |
| 1443 |
- 03 Nov 2006; Fabian Groffen <grobian@g.o> |
| 1444 |
- embassy-emnu-1.05-r2.ebuild, embassy-emnu-1.05-r3.ebuild: |
| 1445 |
- Dropped ppc-macos, see you in prefix. |
| 1446 |
- |
| 1447 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> embassy-emnu-1.05-r3.ebuild: |
| 1448 |
- Added ~sparc |
| 1449 |
- |
| 1450 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 1451 |
- embassy-emnu-1.05-r3.ebuild: |
| 1452 |
- Added to x86. |
| 1453 |
- |
| 1454 |
-*embassy-emnu-1.05-r3 (21 Jul 2006) |
| 1455 |
- |
| 1456 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 1457 |
- +embassy-emnu-1.05-r3.ebuild: |
| 1458 |
- New upstream version building against EMBOSS 4.0.0. |
| 1459 |
- |
| 1460 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 1461 |
- embassy-emnu-1.05-r2.ebuild: |
| 1462 |
- Fixed digest mismatch due to silent upstream repackaging. |
| 1463 |
- |
| 1464 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 1465 |
- -files/embassy-emnu-1.05-r1.patch, -embassy-emnu-1.05-r1.ebuild: |
| 1466 |
- Removed obsolete version. |
| 1467 |
- |
| 1468 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 1469 |
- embassy-emnu-1.05-r2.ebuild: |
| 1470 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 1471 |
- |
| 1472 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 1473 |
- embassy-emnu-1.05-r2.ebuild: |
| 1474 |
- Stable on ppc. |
| 1475 |
- |
| 1476 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 1477 |
- embassy-emnu-1.05-r2.ebuild: |
| 1478 |
- Added to x86. |
| 1479 |
- |
| 1480 |
-*embassy-emnu-1.05-r2 (07 Aug 2005) |
| 1481 |
- |
| 1482 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> |
| 1483 |
- embassy-emnu-1.05-r1.ebuild, +embassy-emnu-1.05-r2.ebuild: |
| 1484 |
- Ported 1.05-r1 to the improved embassy.eclass. The new version is part of |
| 1485 |
- EMBASSY 3.0.0. |
| 1486 |
- |
| 1487 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 1488 |
- -embassy-emnu-1.05.ebuild: |
| 1489 |
- Removed old version. |
| 1490 |
- |
| 1491 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> |
| 1492 |
- embassy-emnu-1.05-r1.ebuild: |
| 1493 |
- Stable ppc-macos |
| 1494 |
- |
| 1495 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> embassy-emnu-1.05-r1.ebuild: |
| 1496 |
- Marked ppc stable. |
| 1497 |
- |
| 1498 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> |
| 1499 |
- embassy-emnu-1.05-r1.ebuild: |
| 1500 |
- Added to x86. |
| 1501 |
- |
| 1502 |
-*embassy-emnu-1.05-r1 (25 Mar 2005) |
| 1503 |
- |
| 1504 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> |
| 1505 |
- +files/embassy-emnu-1.05-r1.patch, +embassy-emnu-1.05-r1.ebuild: |
| 1506 |
- Patched version for EMBOSS 2.10. |
| 1507 |
- |
| 1508 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> embassy-emnu-1.05.ebuild: |
| 1509 |
- Stable ppc-macos |
| 1510 |
- |
| 1511 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-emnu-1.05.ebuild: |
| 1512 |
- Unstable ppc-macos. |
| 1513 |
- |
| 1514 |
-*embassy-emnu-1.05 (23 Dec 2004) |
| 1515 |
- |
| 1516 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 1517 |
- +embassy-emnu-1.05.ebuild: |
| 1518 |
- Moved from app-sci/embassy-emnu to sci-biology/embassy-emnu. |
| 1519 |
- |
| 1520 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> embassy-emnu-1.05.ebuild: |
| 1521 |
- Added to x86. |
| 1522 |
- |
| 1523 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-emnu-1.05.ebuild: |
| 1524 |
- Added to ~ppc. |
| 1525 |
- |
| 1526 |
-* embassy-emnu-1.05 (19 Jul 2004) |
| 1527 |
- |
| 1528 |
- 14 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 1529 |
- embassy-emnu-1.05.ebuild, metadata.xml, ChangeLog |
| 1530 |
- Initial import. |
| 1531 |
|
| 1532 |
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild |
| 1533 |
deleted file mode 100644 |
| 1534 |
index 0291af7..0000000 |
| 1535 |
--- a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild |
| 1536 |
+++ /dev/null |
| 1537 |
@@ -1,17 +0,0 @@ |
| 1538 |
-# Copyright 1999-2015 Gentoo Foundation |
| 1539 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1540 |
-# $Header: $ |
| 1541 |
- |
| 1542 |
-EAPI=5 |
| 1543 |
- |
| 1544 |
-EBO_DESCRIPTION="Simple menu of EMBOSS applications" |
| 1545 |
-EBO_EXTRA_ECONF="$(use_enable ncurses curses)" |
| 1546 |
- |
| 1547 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 1548 |
-AUTOTOOLS_AUTORECONF=1 |
| 1549 |
-inherit emboss-r1 |
| 1550 |
- |
| 1551 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 1552 |
-IUSE+=" ncurses" |
| 1553 |
- |
| 1554 |
-RDEPEND+=" ncurses? ( sys-libs/ncurses )" |
| 1555 |
|
| 1556 |
diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch |
| 1557 |
deleted file mode 100644 |
| 1558 |
index e73eb7b..0000000 |
| 1559 |
--- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch |
| 1560 |
+++ /dev/null |
| 1561 |
@@ -1,127 +0,0 @@ |
| 1562 |
---- EMNU-1.05.650/configure.ac |
| 1563 |
-+++ EMNU-1.05.650/configure.ac |
| 1564 |
-@@ -635,33 +635,6 @@ |
| 1565 |
- |
| 1566 |
- |
| 1567 |
- |
| 1568 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 1569 |
--dnl to see which version's configure.in these lines come from |
| 1570 |
-- |
| 1571 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 1572 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 1573 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 1574 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 1575 |
--dnl that many releases anyway. |
| 1576 |
-- |
| 1577 |
--PCRE_MAJOR="7" |
| 1578 |
--PCRE_MINOR="9" |
| 1579 |
--PCRE_DATE="11-Apr-2009" |
| 1580 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 1581 |
-- |
| 1582 |
--dnl Default values for miscellaneous macros |
| 1583 |
-- |
| 1584 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 1585 |
-- |
| 1586 |
--dnl Provide versioning information for libtool shared libraries that |
| 1587 |
--dnl are built by default on Unix systems. |
| 1588 |
-- |
| 1589 |
--PCRE_LIB_VERSION="0:1:0" |
| 1590 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 1591 |
-- |
| 1592 |
-- |
| 1593 |
-- |
| 1594 |
-- |
| 1595 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 1596 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 1597 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 1598 |
-@@ -737,21 +710,6 @@ |
| 1599 |
- |
| 1600 |
- |
| 1601 |
- |
| 1602 |
--dnl "Export" these variables for PCRE |
| 1603 |
-- |
| 1604 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 1605 |
--AC_SUBST([HAVE_STRERROR]) |
| 1606 |
--AC_SUBST([PCRE_MAJOR]) |
| 1607 |
--AC_SUBST([PCRE_MINOR]) |
| 1608 |
--AC_SUBST([PCRE_DATE]) |
| 1609 |
--AC_SUBST([PCRE_VERSION]) |
| 1610 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 1611 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 1612 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 1613 |
-- |
| 1614 |
-- |
| 1615 |
-- |
| 1616 |
-- |
| 1617 |
- dnl Test if --enable-localforce given |
| 1618 |
- locallink="no" |
| 1619 |
- embprefix="/usr/local" |
| 1620 |
-@@ -874,6 +832,11 @@ |
| 1621 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 1622 |
- |
| 1623 |
- |
| 1624 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 1625 |
-+[ |
| 1626 |
-+dnl using system libraries |
| 1627 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 1628 |
-+]) |
| 1629 |
- |
| 1630 |
- |
| 1631 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 1632 |
-@@ -899,20 +862,16 @@ |
| 1633 |
- |
| 1634 |
- |
| 1635 |
- dnl emnu and mse only: uses curses |
| 1636 |
--dnl Test if --with-curses is given |
| 1637 |
--AC_ARG_WITH([curses], |
| 1638 |
--[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) |
| 1639 |
-- |
| 1640 |
--AC_MSG_CHECKING([for curses]) |
| 1641 |
-- |
| 1642 |
--AS_IF([test "${with_curses}"], |
| 1643 |
--[ |
| 1644 |
-- CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" |
| 1645 |
-- LDFLAGS="$LDFLAGS -L${with_curses}/lib" |
| 1646 |
-+dnl Test if --enable-curses is given |
| 1647 |
-+AC_ARG_ENABLE([curses], |
| 1648 |
-+[AS_HELP_STRING([--enable-curses], [curses])]) |
| 1649 |
-+ |
| 1650 |
-+AS_IF([test "x$enable_curses" = "xyes"], [ |
| 1651 |
-+ PKG_CHECK_MODULES([NCURSES], [ncurses]) |
| 1652 |
-+ PKG_CHECK_MODULES([FORM], [form]) |
| 1653 |
-+ PKG_CHECK_MODULES([MENU], [menu]) |
| 1654 |
- ]) |
| 1655 |
- |
| 1656 |
--AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"]) |
| 1657 |
-- |
| 1658 |
- |
| 1659 |
- |
| 1660 |
- |
| 1661 |
---- EMNU-1.05.650/src/Makefile.am |
| 1662 |
-+++ EMNU-1.05.650/src/Makefile.am |
| 1663 |
-@@ -17,9 +17,8 @@ |
| 1664 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 1665 |
- -I../../../ajax/acd -I../../../plplot |
| 1666 |
- else |
| 1667 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 1668 |
-- $(NLINCLUDES) \ |
| 1669 |
-- -I${embprefix}/include/epcre |
| 1670 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \ |
| 1671 |
-+ $(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS) |
| 1672 |
- endif |
| 1673 |
- |
| 1674 |
- if ISSHARED |
| 1675 |
-@@ -57,5 +56,5 @@ |
| 1676 |
- ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) |
| 1677 |
- else |
| 1678 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 1679 |
-- -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) |
| 1680 |
-+ -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) |
| 1681 |
- endif |
| 1682 |
---- EMNU-1.05.650/emboss_acd/Makefile.am |
| 1683 |
-+++ EMNU-1.05.650/emboss_acd/Makefile.am |
| 1684 |
-@@ -1,3 +1,3 @@ |
| 1685 |
- |
| 1686 |
--pkgdata_DATA = *.acd |
| 1687 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 1688 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 1689 |
|
| 1690 |
diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml |
| 1691 |
deleted file mode 100644 |
| 1692 |
index f17a827..0000000 |
| 1693 |
--- a/sci-biology/embassy-emnu/metadata.xml |
| 1694 |
+++ /dev/null |
| 1695 |
@@ -1,5 +0,0 @@ |
| 1696 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 1697 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 1698 |
-<pkgmetadata> |
| 1699 |
- <herd>sci-biology</herd> |
| 1700 |
-</pkgmetadata> |
| 1701 |
|
| 1702 |
diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog |
| 1703 |
deleted file mode 100644 |
| 1704 |
index 9c25b66..0000000 |
| 1705 |
--- a/sci-biology/embassy-esim4/ChangeLog |
| 1706 |
+++ /dev/null |
| 1707 |
@@ -1,160 +0,0 @@ |
| 1708 |
-# ChangeLog for sci-biology/embassy-esim4 |
| 1709 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 1710 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.28 2010/01/01 21:58:14 fauli Exp $ |
| 1711 |
- |
| 1712 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-esim4-1.0.0-r7.ebuild, |
| 1713 |
- embassy-esim4-1.0.0.650.ebuild, -files/embassy-esim4-1.0.0-r7.patch, |
| 1714 |
- metadata.xml: |
| 1715 |
- Bump eclass, Drop old |
| 1716 |
- |
| 1717 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-esim4-1.0.0-r7.ebuild: |
| 1718 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 1719 |
- |
| 1720 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-esim4-1.0.0-r7.ebuild, |
| 1721 |
- files/embassy-esim4-1.0.0-r7.patch: |
| 1722 |
- Fixed for reviewed eclass |
| 1723 |
- |
| 1724 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-esim4-1.0.0-r7.ebuild: |
| 1725 |
- Naming of eclass changed |
| 1726 |
- |
| 1727 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-esim4-1.0.0-r7.ebuild: |
| 1728 |
- EOV not needed to be set anymore |
| 1729 |
- |
| 1730 |
-*embassy-esim4-1.0.0-r7 (10 Mar 2011) |
| 1731 |
- |
| 1732 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-esim4-1.0.0-r7.ebuild, |
| 1733 |
- +files/embassy-esim4-1.0.0-r7.patch, +metadata.xml: |
| 1734 |
- Move to new embassy-ng.eclass |
| 1735 |
- |
| 1736 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 1737 |
- embassy-esim4-1.0.0-r6.ebuild: |
| 1738 |
- Transfer Prefix keywords |
| 1739 |
- |
| 1740 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 1741 |
- Giving up maintainership of this package. |
| 1742 |
- |
| 1743 |
-*embassy-esim4-1.0.0-r6 (01 Sep 2009) |
| 1744 |
- |
| 1745 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 1746 |
- +embassy-esim4-1.0.0-r6.ebuild: |
| 1747 |
- Updated version for EMBASSY 6.1.0. |
| 1748 |
- |
| 1749 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 1750 |
- embassy-esim4-1.0.0-r5.ebuild: |
| 1751 |
- Stabilised on amd64 and x86. |
| 1752 |
- |
| 1753 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 1754 |
- -embassy-esim4-1.0.0-r4.ebuild: |
| 1755 |
- Pruning version that will never be stabilised. |
| 1756 |
- |
| 1757 |
-*embassy-esim4-1.0.0-r5 (27 Aug 2008) |
| 1758 |
- |
| 1759 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 1760 |
- +embassy-esim4-1.0.0-r5.ebuild: |
| 1761 |
- New upstream version/package for EMBASSY 6.0.1. |
| 1762 |
- |
| 1763 |
-*embassy-esim4-1.0.0-r4 (18 Jul 2007) |
| 1764 |
- |
| 1765 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 1766 |
- +embassy-esim4-1.0.0-r4.ebuild: |
| 1767 |
- New upstream packaging for EMBOSS 5.0.0. |
| 1768 |
- |
| 1769 |
- 16 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 1770 |
- embassy-esim4-1.0.0-r3.ebuild: |
| 1771 |
- Added ~amd64. |
| 1772 |
- |
| 1773 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 1774 |
- -embassy-esim4-1.0.0-r2.ebuild: |
| 1775 |
- Pruning old version. |
| 1776 |
- |
| 1777 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 1778 |
- embassy-esim4-1.0.0-r3.ebuild: |
| 1779 |
- Marked ~sparc |
| 1780 |
- |
| 1781 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 1782 |
- embassy-esim4-1.0.0-r2.ebuild, embassy-esim4-1.0.0-r3.ebuild: |
| 1783 |
- Dropped ppc-macos, see you in prefix. |
| 1784 |
- |
| 1785 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 1786 |
- embassy-esim4-1.0.0-r3.ebuild: |
| 1787 |
- Added to x86. |
| 1788 |
- |
| 1789 |
-*embassy-esim4-1.0.0-r3 (21 Jul 2006) |
| 1790 |
- |
| 1791 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 1792 |
- +embassy-esim4-1.0.0-r3.ebuild: |
| 1793 |
- New upstream version building against EMBOSS 4.0.0. |
| 1794 |
- |
| 1795 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 1796 |
- embassy-esim4-1.0.0-r2.ebuild: |
| 1797 |
- Fixed digest mismatch due to silent upstream repackaging. |
| 1798 |
- |
| 1799 |
- 04 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 1800 |
- -embassy-esim4-1.0.0-r1.ebuild: |
| 1801 |
- Removed obsolete version. |
| 1802 |
- |
| 1803 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 1804 |
- embassy-esim4-1.0.0-r2.ebuild: |
| 1805 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 1806 |
- |
| 1807 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 1808 |
- embassy-esim4-1.0.0-r2.ebuild: |
| 1809 |
- Stable on ppc. |
| 1810 |
- |
| 1811 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 1812 |
- embassy-esim4-1.0.0-r2.ebuild: |
| 1813 |
- Added to x86. |
| 1814 |
- |
| 1815 |
-*embassy-esim4-1.0.0-r2 (07 Aug 2005) |
| 1816 |
- |
| 1817 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> |
| 1818 |
- embassy-esim4-1.0.0-r1.ebuild, +embassy-esim4-1.0.0-r2.ebuild: |
| 1819 |
- Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of |
| 1820 |
- EMBASSY 3.0.0. |
| 1821 |
- |
| 1822 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 1823 |
- -embassy-esim4-1.0.0.ebuild: |
| 1824 |
- Removed old version. |
| 1825 |
- |
| 1826 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> |
| 1827 |
- embassy-esim4-1.0.0-r1.ebuild: |
| 1828 |
- Stable ppc-macos |
| 1829 |
- |
| 1830 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> |
| 1831 |
- embassy-esim4-1.0.0-r1.ebuild: |
| 1832 |
- Marked ppc stable. |
| 1833 |
- |
| 1834 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> |
| 1835 |
- embassy-esim4-1.0.0-r1.ebuild: |
| 1836 |
- Added to x86. |
| 1837 |
- |
| 1838 |
-*embassy-esim4-1.0.0-r1 (25 Mar 2005) |
| 1839 |
- |
| 1840 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> |
| 1841 |
- +embassy-esim4-1.0.0-r1.ebuild: |
| 1842 |
- Build against the EMBOSS 2.10 source tree. |
| 1843 |
- |
| 1844 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> embassy-esim4-1.0.0.ebuild: |
| 1845 |
- Stable ppc-macos |
| 1846 |
- |
| 1847 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-esim4-1.0.0.ebuild: |
| 1848 |
- Unstable ppc-macos. |
| 1849 |
- |
| 1850 |
-*embassy-esim4-1.0.0 (23 Dec 2004) |
| 1851 |
- |
| 1852 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 1853 |
- +embassy-esim4-1.0.0.ebuild: |
| 1854 |
- Moved from app-sci/embassy-esim4 to sci-biology/embassy-esim4. |
| 1855 |
- |
| 1856 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> |
| 1857 |
- embassy-esim4-1.0.0.ebuild: |
| 1858 |
- Added to x86. |
| 1859 |
- |
| 1860 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-esim4-1.0.0.ebuild: |
| 1861 |
- Added to ~ppc. |
| 1862 |
- |
| 1863 |
-* embassy-esim4-1.0.0 (19 Jul 2004) |
| 1864 |
- |
| 1865 |
- 19 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 1866 |
- embassy-esim4-1.0.0.ebuild, metadata.xml, ChangeLog |
| 1867 |
- Initial import. |
| 1868 |
|
| 1869 |
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild |
| 1870 |
deleted file mode 100644 |
| 1871 |
index c6fc9de..0000000 |
| 1872 |
--- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild |
| 1873 |
+++ /dev/null |
| 1874 |
@@ -1,13 +0,0 @@ |
| 1875 |
-# Copyright 1999-2015 Gentoo Foundation |
| 1876 |
-# Distributed under the terms of the GNU General Public License v2 |
| 1877 |
-# $Header: $ |
| 1878 |
- |
| 1879 |
-EAPI=5 |
| 1880 |
- |
| 1881 |
-EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" |
| 1882 |
- |
| 1883 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 1884 |
-AUTOTOOLS_AUTORECONF=1 |
| 1885 |
-inherit emboss-r1 |
| 1886 |
- |
| 1887 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 1888 |
|
| 1889 |
diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch |
| 1890 |
deleted file mode 100644 |
| 1891 |
index 8279071..0000000 |
| 1892 |
--- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch |
| 1893 |
+++ /dev/null |
| 1894 |
@@ -1,97 +0,0 @@ |
| 1895 |
---- ESIM4-1.0.0.650/configure.ac |
| 1896 |
-+++ ESIM4-1.0.0.650/configure.ac |
| 1897 |
-@@ -635,33 +635,6 @@ |
| 1898 |
- |
| 1899 |
- |
| 1900 |
- |
| 1901 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 1902 |
--dnl to see which version's configure.in these lines come from |
| 1903 |
-- |
| 1904 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 1905 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 1906 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 1907 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 1908 |
--dnl that many releases anyway. |
| 1909 |
-- |
| 1910 |
--PCRE_MAJOR="7" |
| 1911 |
--PCRE_MINOR="9" |
| 1912 |
--PCRE_DATE="11-Apr-2009" |
| 1913 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 1914 |
-- |
| 1915 |
--dnl Default values for miscellaneous macros |
| 1916 |
-- |
| 1917 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 1918 |
-- |
| 1919 |
--dnl Provide versioning information for libtool shared libraries that |
| 1920 |
--dnl are built by default on Unix systems. |
| 1921 |
-- |
| 1922 |
--PCRE_LIB_VERSION="0:1:0" |
| 1923 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 1924 |
-- |
| 1925 |
-- |
| 1926 |
-- |
| 1927 |
-- |
| 1928 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 1929 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 1930 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 1931 |
-@@ -737,21 +710,6 @@ |
| 1932 |
- |
| 1933 |
- |
| 1934 |
- |
| 1935 |
--dnl "Export" these variables for PCRE |
| 1936 |
-- |
| 1937 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 1938 |
--AC_SUBST([HAVE_STRERROR]) |
| 1939 |
--AC_SUBST([PCRE_MAJOR]) |
| 1940 |
--AC_SUBST([PCRE_MINOR]) |
| 1941 |
--AC_SUBST([PCRE_DATE]) |
| 1942 |
--AC_SUBST([PCRE_VERSION]) |
| 1943 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 1944 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 1945 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 1946 |
-- |
| 1947 |
-- |
| 1948 |
-- |
| 1949 |
-- |
| 1950 |
- dnl Test if --enable-localforce given |
| 1951 |
- locallink="no" |
| 1952 |
- embprefix="/usr/local" |
| 1953 |
-@@ -874,6 +832,11 @@ |
| 1954 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 1955 |
- |
| 1956 |
- |
| 1957 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 1958 |
-+[ |
| 1959 |
-+dnl using system libraries |
| 1960 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 1961 |
-+]) |
| 1962 |
- |
| 1963 |
- |
| 1964 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 1965 |
---- ESIM4-1.0.0.650/src/Makefile.am |
| 1966 |
-+++ ESIM4-1.0.0.650/src/Makefile.am |
| 1967 |
-@@ -17,9 +17,7 @@ |
| 1968 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 1969 |
- -I../../../ajax/acd -I../../../plplot |
| 1970 |
- else |
| 1971 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 1972 |
-- $(NLINCLUDES) \ |
| 1973 |
-- -I${embprefix}/include/epcre |
| 1974 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 1975 |
- endif |
| 1976 |
- |
| 1977 |
- if ISSHARED |
| 1978 |
-@@ -63,5 +61,5 @@ |
| 1979 |
- $(XLIB) |
| 1980 |
- else |
| 1981 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 1982 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 1983 |
-+ -lajax $(NLADD) $(XLIB) |
| 1984 |
- endif |
| 1985 |
---- ESIM4-1.0.0.650/emboss_acd/Makefile.am |
| 1986 |
-+++ ESIM4-1.0.0.650/emboss_acd/Makefile.am |
| 1987 |
-@@ -1,3 +1,3 @@ |
| 1988 |
- |
| 1989 |
--pkgdata_DATA = *.acd |
| 1990 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 1991 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 1992 |
|
| 1993 |
diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml |
| 1994 |
deleted file mode 100644 |
| 1995 |
index f17a827..0000000 |
| 1996 |
--- a/sci-biology/embassy-esim4/metadata.xml |
| 1997 |
+++ /dev/null |
| 1998 |
@@ -1,5 +0,0 @@ |
| 1999 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 2000 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 2001 |
-<pkgmetadata> |
| 2002 |
- <herd>sci-biology</herd> |
| 2003 |
-</pkgmetadata> |
| 2004 |
|
| 2005 |
diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog |
| 2006 |
deleted file mode 100644 |
| 2007 |
index fa2844c..0000000 |
| 2008 |
--- a/sci-biology/embassy-hmmer/ChangeLog |
| 2009 |
+++ /dev/null |
| 2010 |
@@ -1,166 +0,0 @@ |
| 2011 |
-# ChangeLog for sci-biology/embassy-hmmer |
| 2012 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 2013 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.30 2010/01/01 22:00:05 fauli Exp $ |
| 2014 |
- |
| 2015 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-hmmer-2.3.2-r4.ebuild, |
| 2016 |
- embassy-hmmer-2.3.2.650.ebuild, -files/embassy-hmmer-2.3.2-r4.patch, |
| 2017 |
- metadata.xml: |
| 2018 |
- Bump eclass, Drop old |
| 2019 |
- |
| 2020 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-hmmer-2.3.2-r4.ebuild: |
| 2021 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 2022 |
- |
| 2023 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-hmmer-2.3.2-r4.ebuild, |
| 2024 |
- files/embassy-hmmer-2.3.2-r4.patch: |
| 2025 |
- Fixed for reviewed eclass |
| 2026 |
- |
| 2027 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-hmmer-2.3.2-r4.ebuild: |
| 2028 |
- Naming of eclass changed |
| 2029 |
- |
| 2030 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-hmmer-2.3.2-r4.ebuild: |
| 2031 |
- EOV not needed to be set anymore |
| 2032 |
- |
| 2033 |
-*embassy-hmmer-2.3.2-r4 (10 Mar 2011) |
| 2034 |
- |
| 2035 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-hmmer-2.3.2-r4.ebuild, |
| 2036 |
- +files/embassy-hmmer-2.3.2-r4.patch, +metadata.xml: |
| 2037 |
- Move to new embassy-ng.eclass |
| 2038 |
- |
| 2039 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 2040 |
- embassy-hmmer-2.3.2-r3.ebuild: |
| 2041 |
- Transfer Prefix keywords |
| 2042 |
- |
| 2043 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 2044 |
- Giving up maintainership of this package. |
| 2045 |
- |
| 2046 |
-*embassy-hmmer-2.3.2-r3 (01 Sep 2009) |
| 2047 |
- |
| 2048 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2049 |
- +embassy-hmmer-2.3.2-r3.ebuild: |
| 2050 |
- Updated version for EMBASSY 6.1.0. |
| 2051 |
- |
| 2052 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2053 |
- embassy-hmmer-2.3.2-r2.ebuild: |
| 2054 |
- Stabilised on amd64 and x86. |
| 2055 |
- |
| 2056 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2057 |
- -embassy-hmmer-2.3.2-r1.ebuild: |
| 2058 |
- Pruning version that will never be stabilised. |
| 2059 |
- |
| 2060 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2061 |
- embassy-hmmer-2.3.2-r1.ebuild, embassy-hmmer-2.3.2-r2.ebuild: |
| 2062 |
- Fixed description. Added dependency on HMMER. |
| 2063 |
- |
| 2064 |
-*embassy-hmmer-2.3.2-r2 (27 Aug 2008) |
| 2065 |
- |
| 2066 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2067 |
- +embassy-hmmer-2.3.2-r2.ebuild: |
| 2068 |
- New upstream version/package for EMBASSY 6.0.1. |
| 2069 |
- |
| 2070 |
-*embassy-hmmer-2.3.2-r1 (18 Jul 2007) |
| 2071 |
- |
| 2072 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 2073 |
- +embassy-hmmer-2.3.2-r1.ebuild: |
| 2074 |
- New upstream packaging for EMBOSS 5.0.0. |
| 2075 |
- |
| 2076 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> embassy-hmmer-2.3.2.ebuild: |
| 2077 |
- Added ~amd64 |
| 2078 |
- |
| 2079 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 2080 |
- -embassy-hmmer-2.1.1-r2.ebuild: |
| 2081 |
- Pruning old version. |
| 2082 |
- |
| 2083 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> embassy-hmmer-2.3.2.ebuild: |
| 2084 |
- Added ~sparc |
| 2085 |
- |
| 2086 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 2087 |
- embassy-hmmer-2.1.1-r2.ebuild, embassy-hmmer-2.3.2.ebuild: |
| 2088 |
- Dropped ppc-macos, see you in prefix. |
| 2089 |
- |
| 2090 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 2091 |
- embassy-hmmer-2.3.2.ebuild: |
| 2092 |
- Added to x86. |
| 2093 |
- |
| 2094 |
-*embassy-hmmer-2.3.2 (21 Jul 2006) |
| 2095 |
- |
| 2096 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 2097 |
- embassy-hmmer-2.1.1-r2.ebuild, +embassy-hmmer-2.3.2.ebuild: |
| 2098 |
- New upstream version building against EMBOSS 4.0.0. |
| 2099 |
- |
| 2100 |
- 20 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 2101 |
- embassy-hmmer-2.1.1-r2.ebuild: |
| 2102 |
- Fixed download URL (silent upstream repackaging). |
| 2103 |
- |
| 2104 |
- 04 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 2105 |
- -embassy-hmmer-2.1.1-r1.ebuild: |
| 2106 |
- Removed obsolete version. |
| 2107 |
- |
| 2108 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 2109 |
- embassy-hmmer-2.1.1-r2.ebuild: |
| 2110 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 2111 |
- |
| 2112 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 2113 |
- embassy-hmmer-2.1.1-r2.ebuild: |
| 2114 |
- Stable on ppc. |
| 2115 |
- |
| 2116 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 2117 |
- embassy-hmmer-2.1.1-r2.ebuild: |
| 2118 |
- Added to x86. |
| 2119 |
- |
| 2120 |
-*embassy-hmmer-2.1.1-r2 (07 Aug 2005) |
| 2121 |
- |
| 2122 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> |
| 2123 |
- embassy-hmmer-2.1.1-r1.ebuild, +embassy-hmmer-2.1.1-r2.ebuild: |
| 2124 |
- Ported 2.1.1-r1 to the improved embassy.eclass. The new version is part of |
| 2125 |
- EMBASSY 3.0.0. |
| 2126 |
- |
| 2127 |
- 30 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 2128 |
- embassy-hmmer-2.1.1-r1.ebuild: |
| 2129 |
- Fixed bug #100672. |
| 2130 |
- |
| 2131 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 2132 |
- -embassy-hmmer-2.1.1.ebuild: |
| 2133 |
- Removed old version. |
| 2134 |
- |
| 2135 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> |
| 2136 |
- embassy-hmmer-2.1.1-r1.ebuild: |
| 2137 |
- Stable ppc-macos Bug 96819 |
| 2138 |
- |
| 2139 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> |
| 2140 |
- embassy-hmmer-2.1.1-r1.ebuild: |
| 2141 |
- Marked ppc stable. |
| 2142 |
- |
| 2143 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> |
| 2144 |
- embassy-hmmer-2.1.1-r1.ebuild: |
| 2145 |
- Added to x86. |
| 2146 |
- |
| 2147 |
-*embassy-hmmer-2.1.1-r1 (25 Mar 2005) |
| 2148 |
- |
| 2149 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> |
| 2150 |
- +embassy-hmmer-2.1.1-r1.ebuild: |
| 2151 |
- Build against the EMBOSS 2.10 source tree. |
| 2152 |
- |
| 2153 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> embassy-hmmer-2.1.1.ebuild: |
| 2154 |
- Stable ppc-macos |
| 2155 |
- |
| 2156 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-hmmer-2.1.1.ebuild: |
| 2157 |
- Unstable ppc-macos |
| 2158 |
- |
| 2159 |
-*embassy-hmmer-2.1.1 (23 Dec 2004) |
| 2160 |
- |
| 2161 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 2162 |
- +embassy-hmmer-2.1.1.ebuild: |
| 2163 |
- Moved from app-sci/embassy-hmmer to sci-biology/embassy-hmmer. |
| 2164 |
- |
| 2165 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> |
| 2166 |
- embassy-hmmer-2.1.1.ebuild: |
| 2167 |
- Added to x86. |
| 2168 |
- |
| 2169 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-hmmer-2.1.1.ebuild: |
| 2170 |
- Added to ~ppc. |
| 2171 |
- |
| 2172 |
-* embassy-hmmer-2.1.1 (19 Jul 2004) |
| 2173 |
- |
| 2174 |
- 19 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 2175 |
- embassy-hmmer-2.1.1.ebuild, metadata.xml, ChangeLog |
| 2176 |
- Initial import. |
| 2177 |
|
| 2178 |
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild |
| 2179 |
deleted file mode 100644 |
| 2180 |
index 918e9fd..0000000 |
| 2181 |
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild |
| 2182 |
+++ /dev/null |
| 2183 |
@@ -1,15 +0,0 @@ |
| 2184 |
-# Copyright 1999-2015 Gentoo Foundation |
| 2185 |
-# Distributed under the terms of the GNU General Public License v2 |
| 2186 |
-# $Header: $ |
| 2187 |
- |
| 2188 |
-EAPI=5 |
| 2189 |
- |
| 2190 |
-EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile HMMs" |
| 2191 |
- |
| 2192 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 2193 |
-AUTOTOOLS_AUTORECONF=1 |
| 2194 |
-inherit emboss-r1 |
| 2195 |
- |
| 2196 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 2197 |
- |
| 2198 |
-RDEPEND+="sci-biology/hmmer" |
| 2199 |
|
| 2200 |
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch |
| 2201 |
deleted file mode 100644 |
| 2202 |
index 78d0c25..0000000 |
| 2203 |
--- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch |
| 2204 |
+++ /dev/null |
| 2205 |
@@ -1,90 +0,0 @@ |
| 2206 |
---- HMMER-2.3.2.650/configure.ac |
| 2207 |
-+++ HMMER-2.3.2.650/configure.ac |
| 2208 |
-@@ -635,33 +635,6 @@ |
| 2209 |
- |
| 2210 |
- |
| 2211 |
- |
| 2212 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 2213 |
--dnl to see which version's configure.in these lines come from |
| 2214 |
-- |
| 2215 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 2216 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 2217 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 2218 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 2219 |
--dnl that many releases anyway. |
| 2220 |
-- |
| 2221 |
--PCRE_MAJOR="7" |
| 2222 |
--PCRE_MINOR="9" |
| 2223 |
--PCRE_DATE="11-Apr-2009" |
| 2224 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 2225 |
-- |
| 2226 |
--dnl Default values for miscellaneous macros |
| 2227 |
-- |
| 2228 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 2229 |
-- |
| 2230 |
--dnl Provide versioning information for libtool shared libraries that |
| 2231 |
--dnl are built by default on Unix systems. |
| 2232 |
-- |
| 2233 |
--PCRE_LIB_VERSION="0:1:0" |
| 2234 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 2235 |
-- |
| 2236 |
-- |
| 2237 |
-- |
| 2238 |
-- |
| 2239 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 2240 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 2241 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 2242 |
-@@ -737,21 +710,6 @@ |
| 2243 |
- |
| 2244 |
- |
| 2245 |
- |
| 2246 |
--dnl "Export" these variables for PCRE |
| 2247 |
-- |
| 2248 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 2249 |
--AC_SUBST([HAVE_STRERROR]) |
| 2250 |
--AC_SUBST([PCRE_MAJOR]) |
| 2251 |
--AC_SUBST([PCRE_MINOR]) |
| 2252 |
--AC_SUBST([PCRE_DATE]) |
| 2253 |
--AC_SUBST([PCRE_VERSION]) |
| 2254 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 2255 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 2256 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 2257 |
-- |
| 2258 |
-- |
| 2259 |
-- |
| 2260 |
-- |
| 2261 |
- dnl Test if --enable-localforce given |
| 2262 |
- locallink="no" |
| 2263 |
- embprefix="/usr/local" |
| 2264 |
-@@ -874,6 +832,11 @@ |
| 2265 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 2266 |
- |
| 2267 |
- |
| 2268 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 2269 |
-+[ |
| 2270 |
-+dnl using system libraries |
| 2271 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 2272 |
-+]) |
| 2273 |
- |
| 2274 |
- |
| 2275 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 2276 |
---- HMMER-2.3.2.650/src/Makefile.am |
| 2277 |
-+++ HMMER-2.3.2.650/src/Makefile.am |
| 2278 |
-@@ -17,9 +17,7 @@ |
| 2279 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 2280 |
- -I../../../ajax/acd -I../../../plplot |
| 2281 |
- else |
| 2282 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 2283 |
-- $(NLINCLUDES) \ |
| 2284 |
-- -I${embprefix}/include/epcre |
| 2285 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 2286 |
- endif |
| 2287 |
- |
| 2288 |
- if ISSHARED |
| 2289 |
-@@ -67,5 +65,5 @@ |
| 2290 |
- $(XLIB) |
| 2291 |
- else |
| 2292 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 2293 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 2294 |
-+ -lajax $(NLADD) $(XLIB) |
| 2295 |
- endif |
| 2296 |
|
| 2297 |
diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml |
| 2298 |
deleted file mode 100644 |
| 2299 |
index f17a827..0000000 |
| 2300 |
--- a/sci-biology/embassy-hmmer/metadata.xml |
| 2301 |
+++ /dev/null |
| 2302 |
@@ -1,5 +0,0 @@ |
| 2303 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 2304 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 2305 |
-<pkgmetadata> |
| 2306 |
- <herd>sci-biology</herd> |
| 2307 |
-</pkgmetadata> |
| 2308 |
|
| 2309 |
diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog |
| 2310 |
deleted file mode 100644 |
| 2311 |
index 497766b..0000000 |
| 2312 |
--- a/sci-biology/embassy-iprscan/ChangeLog |
| 2313 |
+++ /dev/null |
| 2314 |
@@ -1,45 +0,0 @@ |
| 2315 |
-# ChangeLog for sci-biology/embassy-iprscan |
| 2316 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 2317 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.5 2010/01/15 22:45:28 fauli Exp $ |
| 2318 |
- |
| 2319 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 2320 |
- -embassy-iprscan-4.3.1-r2.ebuild, embassy-iprscan-4.3.1.650.ebuild, |
| 2321 |
- -files/embassy-iprscan-4.3.1-r2.patch, metadata.xml: |
| 2322 |
- Bump eclass, Drop old |
| 2323 |
- |
| 2324 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-iprscan-4.3.1-r2.ebuild: |
| 2325 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 2326 |
- |
| 2327 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-iprscan-4.3.1-r2.ebuild, |
| 2328 |
- files/embassy-iprscan-4.3.1-r2.patch: |
| 2329 |
- Fixed for reviewed eclass |
| 2330 |
- |
| 2331 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-iprscan-4.3.1-r2.ebuild: |
| 2332 |
- Naming of eclass changed |
| 2333 |
- |
| 2334 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-iprscan-4.3.1-r2.ebuild: |
| 2335 |
- EOV not needed to be set anymore |
| 2336 |
- |
| 2337 |
- 15 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 2338 |
- embassy-iprscan-4.3.1-r1.ebuild: |
| 2339 |
- Transfer Prefix keywords |
| 2340 |
- |
| 2341 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 2342 |
- Giving up maintainership of this package. |
| 2343 |
- |
| 2344 |
-*embassy-iprscan-4.3.1-r1 (01 Sep 2009) |
| 2345 |
- |
| 2346 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2347 |
- +embassy-iprscan-4.3.1-r1.ebuild: |
| 2348 |
- Updated version for EMBASSY 6.1.0. |
| 2349 |
- |
| 2350 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2351 |
- embassy-iprscan-4.3.1.ebuild: |
| 2352 |
- Stabilised on amd64 and x86. |
| 2353 |
- |
| 2354 |
-*embassy-iprscan-4.3.1 (27 Aug 2008) |
| 2355 |
- |
| 2356 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 2357 |
- +embassy-iprscan-4.3.1.ebuild: |
| 2358 |
- Initial import for EMBASSY 6.0.1. |
| 2359 |
- |
| 2360 |
|
| 2361 |
diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild |
| 2362 |
deleted file mode 100644 |
| 2363 |
index a30e837..0000000 |
| 2364 |
--- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild |
| 2365 |
+++ /dev/null |
| 2366 |
@@ -1,13 +0,0 @@ |
| 2367 |
-# Copyright 1999-2015 Gentoo Foundation |
| 2368 |
-# Distributed under the terms of the GNU General Public License v2 |
| 2369 |
-# $Header: $ |
| 2370 |
- |
| 2371 |
-EAPI=5 |
| 2372 |
- |
| 2373 |
-EBO_DESCRIPTION="InterProScan motif detection add-on package" |
| 2374 |
- |
| 2375 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 2376 |
-AUTOTOOLS_AUTORECONF=1 |
| 2377 |
-inherit emboss-r1 |
| 2378 |
- |
| 2379 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
| 2380 |
|
| 2381 |
diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch |
| 2382 |
deleted file mode 100644 |
| 2383 |
index 955005d..0000000 |
| 2384 |
--- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch |
| 2385 |
+++ /dev/null |
| 2386 |
@@ -1,97 +0,0 @@ |
| 2387 |
---- IPRSCAN-4.3.1.650/configure.ac |
| 2388 |
-+++ IPRSCAN-4.3.1.650/configure.ac |
| 2389 |
-@@ -635,33 +635,6 @@ |
| 2390 |
- |
| 2391 |
- |
| 2392 |
- |
| 2393 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 2394 |
--dnl to see which version's configure.in these lines come from |
| 2395 |
-- |
| 2396 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 2397 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 2398 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 2399 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 2400 |
--dnl that many releases anyway. |
| 2401 |
-- |
| 2402 |
--PCRE_MAJOR="7" |
| 2403 |
--PCRE_MINOR="9" |
| 2404 |
--PCRE_DATE="11-Apr-2009" |
| 2405 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 2406 |
-- |
| 2407 |
--dnl Default values for miscellaneous macros |
| 2408 |
-- |
| 2409 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 2410 |
-- |
| 2411 |
--dnl Provide versioning information for libtool shared libraries that |
| 2412 |
--dnl are built by default on Unix systems. |
| 2413 |
-- |
| 2414 |
--PCRE_LIB_VERSION="0:1:0" |
| 2415 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 2416 |
-- |
| 2417 |
-- |
| 2418 |
-- |
| 2419 |
-- |
| 2420 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 2421 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 2422 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 2423 |
-@@ -737,21 +710,6 @@ |
| 2424 |
- |
| 2425 |
- |
| 2426 |
- |
| 2427 |
--dnl "Export" these variables for PCRE |
| 2428 |
-- |
| 2429 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 2430 |
--AC_SUBST([HAVE_STRERROR]) |
| 2431 |
--AC_SUBST([PCRE_MAJOR]) |
| 2432 |
--AC_SUBST([PCRE_MINOR]) |
| 2433 |
--AC_SUBST([PCRE_DATE]) |
| 2434 |
--AC_SUBST([PCRE_VERSION]) |
| 2435 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 2436 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 2437 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 2438 |
-- |
| 2439 |
-- |
| 2440 |
-- |
| 2441 |
-- |
| 2442 |
- dnl Test if --enable-localforce given |
| 2443 |
- locallink="no" |
| 2444 |
- embprefix="/usr/local" |
| 2445 |
-@@ -874,6 +832,11 @@ |
| 2446 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 2447 |
- |
| 2448 |
- |
| 2449 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 2450 |
-+[ |
| 2451 |
-+dnl using system libraries |
| 2452 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 2453 |
-+]) |
| 2454 |
- |
| 2455 |
- |
| 2456 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 2457 |
---- IPRSCAN-4.3.1.650/src/Makefile.am |
| 2458 |
-+++ IPRSCAN-4.3.1.650/src/Makefile.am |
| 2459 |
-@@ -17,9 +17,7 @@ |
| 2460 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 2461 |
- -I../../../ajax/acd -I../../../plplot |
| 2462 |
- else |
| 2463 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 2464 |
-- $(NLINCLUDES) \ |
| 2465 |
-- -I${embprefix}/include/epcre |
| 2466 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 2467 |
- endif |
| 2468 |
- |
| 2469 |
- if ISSHARED |
| 2470 |
-@@ -58,5 +56,5 @@ |
| 2471 |
- $(XLIB) |
| 2472 |
- else |
| 2473 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 2474 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 2475 |
-+ -lajax $(NLADD) $(XLIB) |
| 2476 |
- endif |
| 2477 |
---- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am |
| 2478 |
-+++ IPRSCAN-4.3.1.650/emboss_acd/Makefile.am |
| 2479 |
-@@ -1,3 +1,3 @@ |
| 2480 |
- |
| 2481 |
--pkgdata_DATA = *.acd |
| 2482 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 2483 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 2484 |
|
| 2485 |
diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml |
| 2486 |
deleted file mode 100644 |
| 2487 |
index f17a827..0000000 |
| 2488 |
--- a/sci-biology/embassy-iprscan/metadata.xml |
| 2489 |
+++ /dev/null |
| 2490 |
@@ -1,5 +0,0 @@ |
| 2491 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 2492 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 2493 |
-<pkgmetadata> |
| 2494 |
- <herd>sci-biology</herd> |
| 2495 |
-</pkgmetadata> |
| 2496 |
|
| 2497 |
diff --git a/sci-biology/embassy-meme/ChangeLog b/sci-biology/embassy-meme/ChangeLog |
| 2498 |
deleted file mode 100644 |
| 2499 |
index 746ddda..0000000 |
| 2500 |
--- a/sci-biology/embassy-meme/ChangeLog |
| 2501 |
+++ /dev/null |
| 2502 |
@@ -1,75 +0,0 @@ |
| 2503 |
-# ChangeLog for sci-biology/embassy-meme |
| 2504 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 2505 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-memenew/ChangeLog,v 1.11 2010/01/01 22:03:00 fauli Exp $ |
| 2506 |
- |
| 2507 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> embassy-meme-4.7.650.ebuild, |
| 2508 |
- metadata.xml: |
| 2509 |
- Bump eclass, Drop old |
| 2510 |
- |
| 2511 |
- 14 Jan 2012; Andreas K. Huettel <dilfridge@g.o> |
| 2512 |
- -embassy-memenew-4.0.0-r1.ebuild: |
| 2513 |
- Removed because the file is non-fetchable |
| 2514 |
- |
| 2515 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-memenew-4.0.0-r1.ebuild: |
| 2516 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 2517 |
- |
| 2518 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-memenew-4.0.0-r1.ebuild, |
| 2519 |
- files/embassy-memenew-4.0.0-r1.patch: |
| 2520 |
- Fixed for reviewed eclass |
| 2521 |
- |
| 2522 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-memenew-4.0.0-r1.ebuild: |
| 2523 |
- Naming of eclass changed |
| 2524 |
- |
| 2525 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-memenew-4.0.0-r1.ebuild: |
| 2526 |
- EOV not needed to be set anymore |
| 2527 |
- |
| 2528 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 2529 |
- embassy-memenew-4.0.0.ebuild: |
| 2530 |
- Transfer Prefix keywords |
| 2531 |
- |
| 2532 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 2533 |
- Giving up maintainership of this package. |
| 2534 |
- |
| 2535 |
-*embassy-memenew-4.0.0 (01 Sep 2009) |
| 2536 |
- |
| 2537 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2538 |
- +embassy-memenew-4.0.0.ebuild: |
| 2539 |
- Updated version for EMBASSY 6.1.0. |
| 2540 |
- |
| 2541 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2542 |
- embassy-memenew-0.1.0-r1.ebuild: |
| 2543 |
- Stabilised on amd64 and x86. |
| 2544 |
- |
| 2545 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2546 |
- embassy-memenew-0.1.0.ebuild, embassy-memenew-0.1.0-r1.ebuild: |
| 2547 |
- Fixed description. |
| 2548 |
- |
| 2549 |
-*embassy-memenew-0.1.0-r1 (27 Aug 2008) |
| 2550 |
- |
| 2551 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2552 |
- +embassy-memenew-0.1.0-r1.ebuild: |
| 2553 |
- New upstream version/package for EMBASSY 6.0.1. |
| 2554 |
- |
| 2555 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 2556 |
- embassy-memenew-0.1.0.ebuild: |
| 2557 |
- Added ~amd64. |
| 2558 |
- |
| 2559 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 2560 |
- embassy-memenew-0.1.0.ebuild: |
| 2561 |
- Added ~sparc |
| 2562 |
- |
| 2563 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 2564 |
- embassy-memenew-0.1.0.ebuild: |
| 2565 |
- Dropped ppc-macos, see you in prefix. |
| 2566 |
- |
| 2567 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 2568 |
- embassy-memenew-0.1.0.ebuild: |
| 2569 |
- Added to x86. |
| 2570 |
- |
| 2571 |
-*embassy-memenew-0.1.0 (21 Jul 2006) |
| 2572 |
- |
| 2573 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 2574 |
- +embassy-memenew-0.1.0.ebuild: |
| 2575 |
- Initial import. This package will probably replace EMBASSY-MEME in new |
| 2576 |
- EMBASSY releases. |
| 2577 |
- |
| 2578 |
|
| 2579 |
diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild |
| 2580 |
deleted file mode 100644 |
| 2581 |
index 473b7c5..0000000 |
| 2582 |
--- a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild |
| 2583 |
+++ /dev/null |
| 2584 |
@@ -1,15 +0,0 @@ |
| 2585 |
-# Copyright 1999-2015 Gentoo Foundation |
| 2586 |
-# Distributed under the terms of the GNU General Public License v2 |
| 2587 |
-# $Header: $ |
| 2588 |
- |
| 2589 |
-EAPI=5 |
| 2590 |
- |
| 2591 |
-EBO_DESCRIPTION="wrappers for MEME - Multiple Em for Motif Elicitation" |
| 2592 |
- |
| 2593 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 2594 |
-AUTOTOOLS_AUTORECONF=1 |
| 2595 |
-inherit emboss-r1 |
| 2596 |
- |
| 2597 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
| 2598 |
- |
| 2599 |
-RDEPEND+=" sci-biology/meme" |
| 2600 |
|
| 2601 |
diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch |
| 2602 |
deleted file mode 100644 |
| 2603 |
index 03c4246..0000000 |
| 2604 |
--- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch |
| 2605 |
+++ /dev/null |
| 2606 |
@@ -1,90 +0,0 @@ |
| 2607 |
---- MEME-4.7.650/configure.ac |
| 2608 |
-+++ MEME-4.7.650/configure.ac |
| 2609 |
-@@ -635,33 +635,6 @@ |
| 2610 |
- |
| 2611 |
- |
| 2612 |
- |
| 2613 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 2614 |
--dnl to see which version's configure.in these lines come from |
| 2615 |
-- |
| 2616 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 2617 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 2618 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 2619 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 2620 |
--dnl that many releases anyway. |
| 2621 |
-- |
| 2622 |
--PCRE_MAJOR="7" |
| 2623 |
--PCRE_MINOR="9" |
| 2624 |
--PCRE_DATE="11-Apr-2009" |
| 2625 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 2626 |
-- |
| 2627 |
--dnl Default values for miscellaneous macros |
| 2628 |
-- |
| 2629 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 2630 |
-- |
| 2631 |
--dnl Provide versioning information for libtool shared libraries that |
| 2632 |
--dnl are built by default on Unix systems. |
| 2633 |
-- |
| 2634 |
--PCRE_LIB_VERSION="0:1:0" |
| 2635 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 2636 |
-- |
| 2637 |
-- |
| 2638 |
-- |
| 2639 |
-- |
| 2640 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 2641 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 2642 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 2643 |
-@@ -737,21 +710,6 @@ |
| 2644 |
- |
| 2645 |
- |
| 2646 |
- |
| 2647 |
--dnl "Export" these variables for PCRE |
| 2648 |
-- |
| 2649 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 2650 |
--AC_SUBST([HAVE_STRERROR]) |
| 2651 |
--AC_SUBST([PCRE_MAJOR]) |
| 2652 |
--AC_SUBST([PCRE_MINOR]) |
| 2653 |
--AC_SUBST([PCRE_DATE]) |
| 2654 |
--AC_SUBST([PCRE_VERSION]) |
| 2655 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 2656 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 2657 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 2658 |
-- |
| 2659 |
-- |
| 2660 |
-- |
| 2661 |
-- |
| 2662 |
- dnl Test if --enable-localforce given |
| 2663 |
- locallink="no" |
| 2664 |
- embprefix="/usr/local" |
| 2665 |
-@@ -874,6 +832,11 @@ |
| 2666 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 2667 |
- |
| 2668 |
- |
| 2669 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 2670 |
-+[ |
| 2671 |
-+dnl using system libraries |
| 2672 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 2673 |
-+]) |
| 2674 |
- |
| 2675 |
- |
| 2676 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 2677 |
---- MEME-4.7.650/src/Makefile.am |
| 2678 |
-+++ MEME-4.7.650/src/Makefile.am |
| 2679 |
-@@ -17,9 +17,7 @@ |
| 2680 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 2681 |
- -I../../../ajax/acd -I../../../plplot |
| 2682 |
- else |
| 2683 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 2684 |
-- $(NLINCLUDES) \ |
| 2685 |
-- -I${embprefix}/include/epcre |
| 2686 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 2687 |
- endif |
| 2688 |
- |
| 2689 |
- if ISSHARED |
| 2690 |
-@@ -60,5 +58,5 @@ |
| 2691 |
- $(XLIB) |
| 2692 |
- else |
| 2693 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 2694 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 2695 |
-+ -lajax $(NLADD) $(XLIB) |
| 2696 |
- endif |
| 2697 |
|
| 2698 |
diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml |
| 2699 |
deleted file mode 100644 |
| 2700 |
index f17a827..0000000 |
| 2701 |
--- a/sci-biology/embassy-meme/metadata.xml |
| 2702 |
+++ /dev/null |
| 2703 |
@@ -1,5 +0,0 @@ |
| 2704 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 2705 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 2706 |
-<pkgmetadata> |
| 2707 |
- <herd>sci-biology</herd> |
| 2708 |
-</pkgmetadata> |
| 2709 |
|
| 2710 |
diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog |
| 2711 |
deleted file mode 100644 |
| 2712 |
index 1316099..0000000 |
| 2713 |
--- a/sci-biology/embassy-mse/ChangeLog |
| 2714 |
+++ /dev/null |
| 2715 |
@@ -1,185 +0,0 @@ |
| 2716 |
-# ChangeLog for sci-biology/embassy-mse |
| 2717 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 2718 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.35 2010/01/01 22:05:28 fauli Exp $ |
| 2719 |
- |
| 2720 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-mse-3.0.0.ebuild, |
| 2721 |
- embassy-mse-3.0.0.650.ebuild, -files/embassy-mse-3.0.0.patch, metadata.xml: |
| 2722 |
- Bump eclass, drop old |
| 2723 |
- |
| 2724 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-mse-3.0.0.ebuild: |
| 2725 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 2726 |
- |
| 2727 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-mse-3.0.0.ebuild, |
| 2728 |
- files/embassy-mse-3.0.0.patch: |
| 2729 |
- Fixed for reviewed eclass |
| 2730 |
- |
| 2731 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-mse-3.0.0.ebuild: |
| 2732 |
- Naming of eclass changed |
| 2733 |
- |
| 2734 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-mse-3.0.0.ebuild: |
| 2735 |
- EOV not needed to be set anymore |
| 2736 |
- |
| 2737 |
-*embassy-mse-3.0.0 (10 Mar 2011) |
| 2738 |
- |
| 2739 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-mse-3.0.0.ebuild, |
| 2740 |
- +files/embassy-mse-3.0.0.patch, +metadata.xml: |
| 2741 |
- Version Bump, Move to new embassy-ng.eclass |
| 2742 |
- |
| 2743 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 2744 |
- embassy-mse-1.0.0-r7.ebuild: |
| 2745 |
- Transfer Prefix keywords |
| 2746 |
- |
| 2747 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 2748 |
- Giving up maintainership of this package. |
| 2749 |
- |
| 2750 |
-*embassy-mse-1.0.0-r7 (01 Sep 2009) |
| 2751 |
- |
| 2752 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2753 |
- +embassy-mse-1.0.0-r7.ebuild: |
| 2754 |
- Updated version for EMBASSY 6.1.0. |
| 2755 |
- |
| 2756 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 2757 |
- embassy-mse-1.0.0-r6.ebuild: |
| 2758 |
- Stabilised on amd64 and x86. |
| 2759 |
- |
| 2760 |
- 28 Aug 2008; Olivier Fisette <ribosome@g.o> ChangeLog: |
| 2761 |
- Fixing broken Manifest. |
| 2762 |
- |
| 2763 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2764 |
- -embassy-mse-1.0.0-r5.ebuild: |
| 2765 |
- Pruning version that will never be stabilised. |
| 2766 |
- |
| 2767 |
-*embassy-mse-1.0.0-r6 (27 Aug 2008) |
| 2768 |
- |
| 2769 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 2770 |
- +embassy-mse-1.0.0-r6.ebuild: |
| 2771 |
- New upstream version/package for EMBASSY 6.0.1. |
| 2772 |
- |
| 2773 |
- 07 Aug 2007; Olivier Fisette <ribosome@g.o> |
| 2774 |
- embassy-mse-1.0.0-r5.ebuild: |
| 2775 |
- Removed multilib-strict fix, as it was moved to the embassy eclass. |
| 2776 |
- |
| 2777 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 2778 |
- +embassy-mse-1.0.0-r4.ebuild: |
| 2779 |
- We still need an AMD64 ebuild for EMBOSS 4.0.0 (my mistake). |
| 2780 |
- |
| 2781 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 2782 |
- -embassy-mse-1.0.0-r4.ebuild: |
| 2783 |
- Pruned old version that will never be stabilised. |
| 2784 |
- |
| 2785 |
-*embassy-mse-1.0.0-r5 (18 Jul 2007) |
| 2786 |
- |
| 2787 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 2788 |
- +embassy-mse-1.0.0-r5.ebuild: |
| 2789 |
- New upstream packaging for EMBOSS 5.0.0. |
| 2790 |
- |
| 2791 |
- 17 Feb 2007; Olivier Fisette <ribosome@g.o> |
| 2792 |
- embassy-mse-1.0.0-r4.ebuild: |
| 2793 |
- Added to ~amd64. |
| 2794 |
- |
| 2795 |
-*embassy-mse-1.0.0-r4 (17 Feb 2007) |
| 2796 |
- |
| 2797 |
- 17 Feb 2007; Olivier Fisette <ribosome@g.o> |
| 2798 |
- +embassy-mse-1.0.0-r4.ebuild: |
| 2799 |
- Added a fix for multilib-strict on AMD64 suggested by Jeff Gardner |
| 2800 |
- <je_fro@g.o>. |
| 2801 |
- |
| 2802 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 2803 |
- -embassy-mse-1.0.0-r2.ebuild: |
| 2804 |
- Pruning old version. |
| 2805 |
- |
| 2806 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-mse-1.0.0-r3.ebuild: |
| 2807 |
- Stable on ppc wrt bug 153766 |
| 2808 |
- |
| 2809 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> embassy-mse-1.0.0-r3.ebuild: |
| 2810 |
- Added ~sparc |
| 2811 |
- |
| 2812 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 2813 |
- embassy-mse-1.0.0-r2.ebuild, embassy-mse-1.0.0-r3.ebuild: |
| 2814 |
- Dropped ppc-macos, see you in prefix. |
| 2815 |
- |
| 2816 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 2817 |
- embassy-mse-1.0.0-r3.ebuild: |
| 2818 |
- Added to x86. |
| 2819 |
- |
| 2820 |
-*embassy-mse-1.0.0-r3 (21 Jul 2006) |
| 2821 |
- |
| 2822 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 2823 |
- +embassy-mse-1.0.0-r3.ebuild: |
| 2824 |
- New upstream version building against EMBOSS 4.0.0. |
| 2825 |
- |
| 2826 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 2827 |
- embassy-mse-1.0.0-r2.ebuild: |
| 2828 |
- Fixed download URL (silent upstream repackaging). |
| 2829 |
- |
| 2830 |
- 04 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 2831 |
- -embassy-mse-1.0.0-r1.ebuild: |
| 2832 |
- Removed obsolete version. |
| 2833 |
- |
| 2834 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 2835 |
- embassy-mse-1.0.0-r2.ebuild: |
| 2836 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 2837 |
- |
| 2838 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 2839 |
- embassy-mse-1.0.0-r2.ebuild: |
| 2840 |
- Stable on ppc. |
| 2841 |
- |
| 2842 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 2843 |
- embassy-mse-1.0.0-r2.ebuild: |
| 2844 |
- Added to x86. |
| 2845 |
- |
| 2846 |
-*embassy-mse-1.0.0-r2 (07 Aug 2005) |
| 2847 |
- |
| 2848 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> |
| 2849 |
- embassy-mse-1.0.0-r1.ebuild, +embassy-mse-1.0.0-r2.ebuild: |
| 2850 |
- Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of |
| 2851 |
- EMBASSY 3.0.0. |
| 2852 |
- |
| 2853 |
- 30 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 2854 |
- embassy-mse-1.0.0-r1.ebuild: |
| 2855 |
- Fixed bug #100672. |
| 2856 |
- |
| 2857 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 2858 |
- -embassy-mse-1.0.0.ebuild: |
| 2859 |
- Removed old version. |
| 2860 |
- |
| 2861 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> |
| 2862 |
- embassy-mse-1.0.0-r1.ebuild: |
| 2863 |
- Stable ppc-macos Bug 96819 |
| 2864 |
- |
| 2865 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> embassy-mse-1.0.0-r1.ebuild: |
| 2866 |
- Marked ppc stable. |
| 2867 |
- |
| 2868 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> |
| 2869 |
- embassy-mse-1.0.0-r1.ebuild: |
| 2870 |
- Added to x86. |
| 2871 |
- |
| 2872 |
-*embassy-mse-1.0.0-r1 (25 Mar 2005) |
| 2873 |
- |
| 2874 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> |
| 2875 |
- +embassy-mse-1.0.0-r1.ebuild: |
| 2876 |
- Build against the EMBOSS 2.10 source tree. |
| 2877 |
- |
| 2878 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> embassy-mse-1.0.0.ebuild: |
| 2879 |
- Stable ppc-macos |
| 2880 |
- |
| 2881 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-mse-1.0.0.ebuild: |
| 2882 |
- Unstable ppc-macos |
| 2883 |
- |
| 2884 |
-*embassy-mse-1.0.0 (23 Dec 2004) |
| 2885 |
- |
| 2886 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 2887 |
- +embassy-mse-1.0.0.ebuild: |
| 2888 |
- Moved from app-sci/embassy-mse to sci-biology/embassy-mse. |
| 2889 |
- |
| 2890 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> embassy-mse-1.0.0.ebuild: |
| 2891 |
- Added to x86. |
| 2892 |
- |
| 2893 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-mse-1.0.0.ebuild: |
| 2894 |
- Added to ~ppc. |
| 2895 |
- |
| 2896 |
-* embassy-mse-1.0.0 (19 Jul 2004) |
| 2897 |
- |
| 2898 |
- 19 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 2899 |
- embassy-mse-1.0.0.ebuild, metadata.xml, ChangeLog |
| 2900 |
- Initial import. |
| 2901 |
|
| 2902 |
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild |
| 2903 |
deleted file mode 100644 |
| 2904 |
index d77af20..0000000 |
| 2905 |
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild |
| 2906 |
+++ /dev/null |
| 2907 |
@@ -1,23 +0,0 @@ |
| 2908 |
-# Copyright 1999-2015 Gentoo Foundation |
| 2909 |
-# Distributed under the terms of the GNU General Public License v2 |
| 2910 |
-# $Header: $ |
| 2911 |
- |
| 2912 |
-EAPI=5 |
| 2913 |
- |
| 2914 |
-EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" |
| 2915 |
-EBO_EXTRA_ECONF="$(use_enable ncurses curses)" |
| 2916 |
- |
| 2917 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 2918 |
-AUTOTOOLS_AUTORECONF=1 |
| 2919 |
-inherit emboss-r1 |
| 2920 |
- |
| 2921 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 2922 |
-IUSE+=" ncurses" |
| 2923 |
- |
| 2924 |
-RDEPEND+=" ncurses? ( sys-libs/ncurses )" |
| 2925 |
- |
| 2926 |
-src_install() { |
| 2927 |
- emboss-r1_src_install |
| 2928 |
- insinto /usr/include/emboss/mse |
| 2929 |
- doins h/*.h |
| 2930 |
-} |
| 2931 |
|
| 2932 |
diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch |
| 2933 |
deleted file mode 100644 |
| 2934 |
index 8b2f057..0000000 |
| 2935 |
--- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch |
| 2936 |
+++ /dev/null |
| 2937 |
@@ -1,133 +0,0 @@ |
| 2938 |
---- MSE-3.0.0.650/configure.ac |
| 2939 |
-+++ MSE-3.0.0.650/configure.ac |
| 2940 |
-@@ -635,33 +635,6 @@ |
| 2941 |
- |
| 2942 |
- |
| 2943 |
- |
| 2944 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 2945 |
--dnl to see which version's configure.in these lines come from |
| 2946 |
-- |
| 2947 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 2948 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 2949 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 2950 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 2951 |
--dnl that many releases anyway. |
| 2952 |
-- |
| 2953 |
--PCRE_MAJOR="7" |
| 2954 |
--PCRE_MINOR="9" |
| 2955 |
--PCRE_DATE="11-Apr-2009" |
| 2956 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 2957 |
-- |
| 2958 |
--dnl Default values for miscellaneous macros |
| 2959 |
-- |
| 2960 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 2961 |
-- |
| 2962 |
--dnl Provide versioning information for libtool shared libraries that |
| 2963 |
--dnl are built by default on Unix systems. |
| 2964 |
-- |
| 2965 |
--PCRE_LIB_VERSION="0:1:0" |
| 2966 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 2967 |
-- |
| 2968 |
-- |
| 2969 |
-- |
| 2970 |
-- |
| 2971 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 2972 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 2973 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 2974 |
-@@ -737,21 +710,6 @@ |
| 2975 |
- |
| 2976 |
- |
| 2977 |
- |
| 2978 |
--dnl "Export" these variables for PCRE |
| 2979 |
-- |
| 2980 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 2981 |
--AC_SUBST([HAVE_STRERROR]) |
| 2982 |
--AC_SUBST([PCRE_MAJOR]) |
| 2983 |
--AC_SUBST([PCRE_MINOR]) |
| 2984 |
--AC_SUBST([PCRE_DATE]) |
| 2985 |
--AC_SUBST([PCRE_VERSION]) |
| 2986 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 2987 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 2988 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 2989 |
-- |
| 2990 |
-- |
| 2991 |
-- |
| 2992 |
-- |
| 2993 |
- dnl Test if --enable-localforce given |
| 2994 |
- locallink="no" |
| 2995 |
- embprefix="/usr/local" |
| 2996 |
-@@ -874,6 +832,11 @@ |
| 2997 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 2998 |
- |
| 2999 |
- |
| 3000 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 3001 |
-+[ |
| 3002 |
-+dnl using system libraries |
| 3003 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 3004 |
-+]) |
| 3005 |
- |
| 3006 |
- |
| 3007 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 3008 |
-@@ -1000,17 +963,13 @@ |
| 3009 |
- |
| 3010 |
- |
| 3011 |
- |
| 3012 |
--dnl emnu and mse only: uses curses |
| 3013 |
--dnl Test if --with-curses is given |
| 3014 |
--AC_ARG_WITH([curses], |
| 3015 |
-- [AS_HELP_STRING([--with-curses], |
| 3016 |
-- [curses (or ncurses)])]) |
| 3017 |
--if test "${with_curses}" ; then |
| 3018 |
--AC_MSG_CHECKING([for curses]) |
| 3019 |
--CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" |
| 3020 |
--LDFLAGS="$LDFLAGS -L${with_curses}/lib" |
| 3021 |
--fi |
| 3022 |
--AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") |
| 3023 |
-+dnl Test if --enable-curses is given |
| 3024 |
-+AC_ARG_ENABLE([curses], |
| 3025 |
-+[AS_HELP_STRING([--enable-curses], [curses])]) |
| 3026 |
-+ |
| 3027 |
-+AS_IF([test "x$enable_curses" = "xyes"], [ |
| 3028 |
-+ PKG_CHECK_MODULES([NCURSES], [ncurses]) |
| 3029 |
-+]) |
| 3030 |
- |
| 3031 |
- |
| 3032 |
- |
| 3033 |
---- MSE-3.0.0.650/src/Makefile.am |
| 3034 |
-+++ MSE-3.0.0.650/src/Makefile.am |
| 3035 |
-@@ -18,9 +18,7 @@ |
| 3036 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 3037 |
- -I../../../ajax/acd -I../../../plplot |
| 3038 |
- else |
| 3039 |
--AM_CPPFLAGS = -I../h -I${embprefix}/include \ |
| 3040 |
-- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ |
| 3041 |
-- $(NLINCLUDES) |
| 3042 |
-+AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) |
| 3043 |
- endif |
| 3044 |
- |
| 3045 |
- if ISSHARED |
| 3046 |
-@@ -60,5 +58,5 @@ |
| 3047 |
- $(XLIB) |
| 3048 |
- else |
| 3049 |
- LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ |
| 3050 |
-- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 3051 |
-+ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) |
| 3052 |
- endif |
| 3053 |
---- MSE-3.0.0.650/ckit/Makefile.am |
| 3054 |
-+++ MSE-3.0.0.650/ckit/Makefile.am |
| 3055 |
-@@ -2,7 +2,7 @@ |
| 3056 |
- |
| 3057 |
- lib_LTLIBRARIES = libckit.la |
| 3058 |
- |
| 3059 |
--AM_CPPFLAGS = -I../h |
| 3060 |
-+AM_CPPFLAGS = -I$(top_srcdir)/h |
| 3061 |
- |
| 3062 |
- CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ |
| 3063 |
- seqspec.c ttyinterface.c nextseqentry.c \ |
| 3064 |
---- MSE-3.0.0.650/emboss_acd/Makefile.am |
| 3065 |
-+++ MSE-3.0.0.650/emboss_acd/Makefile.am |
| 3066 |
-@@ -1,3 +1,3 @@ |
| 3067 |
- |
| 3068 |
--pkgdata_DATA = *.acd |
| 3069 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 3070 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 3071 |
|
| 3072 |
diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml |
| 3073 |
deleted file mode 100644 |
| 3074 |
index f17a827..0000000 |
| 3075 |
--- a/sci-biology/embassy-mse/metadata.xml |
| 3076 |
+++ /dev/null |
| 3077 |
@@ -1,5 +0,0 @@ |
| 3078 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 3079 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 3080 |
-<pkgmetadata> |
| 3081 |
- <herd>sci-biology</herd> |
| 3082 |
-</pkgmetadata> |
| 3083 |
|
| 3084 |
diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog |
| 3085 |
deleted file mode 100644 |
| 3086 |
index 7c9443a..0000000 |
| 3087 |
--- a/sci-biology/embassy-phylipnew/ChangeLog |
| 3088 |
+++ /dev/null |
| 3089 |
@@ -1,81 +0,0 @@ |
| 3090 |
-# ChangeLog for sci-biology/embassy-phylipnew |
| 3091 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 3092 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $ |
| 3093 |
- |
| 3094 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-phylipnew-3.69.ebuild, |
| 3095 |
- embassy-phylipnew-3.69.650.ebuild, -files/embassy-phylipnew-3.69.patch, |
| 3096 |
- metadata.xml: |
| 3097 |
- Bump eclass, drop old |
| 3098 |
- |
| 3099 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-phylipnew-3.69.ebuild: |
| 3100 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 3101 |
- |
| 3102 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-phylipnew-3.69.ebuild, |
| 3103 |
- files/embassy-phylipnew-3.69.patch: |
| 3104 |
- Fixed for reviewed eclass |
| 3105 |
- |
| 3106 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-phylipnew-3.69.ebuild: |
| 3107 |
- Naming of eclass changed |
| 3108 |
- |
| 3109 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-phylipnew-3.69.ebuild: |
| 3110 |
- EOV not needed to be set anymore |
| 3111 |
- |
| 3112 |
-*embassy-phylipnew-3.69 (10 Mar 2011) |
| 3113 |
- |
| 3114 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-phylipnew-3.69.ebuild, |
| 3115 |
- +files/embassy-phylipnew-3.69.patch, +metadata.xml: |
| 3116 |
- Version Bump, Move to new embassy-ng.eclass |
| 3117 |
- |
| 3118 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 3119 |
- embassy-phylipnew-3.68.ebuild: |
| 3120 |
- Transfer Prefix keywords |
| 3121 |
- |
| 3122 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 3123 |
- Giving up maintainership of this package. |
| 3124 |
- |
| 3125 |
-*embassy-phylipnew-3.68 (01 Sep 2009) |
| 3126 |
- |
| 3127 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3128 |
- +embassy-phylipnew-3.68.ebuild: |
| 3129 |
- Updated version for EMBASSY 6.1.0. |
| 3130 |
- |
| 3131 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3132 |
- embassy-phylipnew-3.67.ebuild: |
| 3133 |
- Stabilised on amd64 and x86. |
| 3134 |
- |
| 3135 |
-*embassy-phylipnew-3.67 (27 Aug 2008) |
| 3136 |
- |
| 3137 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3138 |
- +embassy-phylipnew-3.67.ebuild: |
| 3139 |
- New upstream version/package for EMBASSY 6.0.1. |
| 3140 |
- |
| 3141 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3142 |
- embassy-phylipnew-3.6b.ebuild: |
| 3143 |
- Fixed description. |
| 3144 |
- |
| 3145 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 3146 |
- embassy-phylipnew-3.6b.ebuild: |
| 3147 |
- Adding ~amd64. |
| 3148 |
- |
| 3149 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-phylipnew-3.6b.ebuild: |
| 3150 |
- Stable on ppc wrt bug 153766 |
| 3151 |
- |
| 3152 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 3153 |
- embassy-phylipnew-3.6b.ebuild: |
| 3154 |
- Added ~sparc |
| 3155 |
- |
| 3156 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 3157 |
- embassy-phylipnew-3.6b.ebuild: |
| 3158 |
- Dropped ppc-macos, see you in prefix. |
| 3159 |
- |
| 3160 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 3161 |
- embassy-phylipnew-3.6b.ebuild: |
| 3162 |
- Added to x86. |
| 3163 |
- |
| 3164 |
-*embassy-phylipnew-3.6b (21 Jul 2006) |
| 3165 |
- |
| 3166 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 3167 |
- +embassy-phylipnew-3.6b.ebuild: |
| 3168 |
- Initial import. This package will probably replace EMBASSY-PHYLIP in new |
| 3169 |
- EMBASSY releases. |
| 3170 |
- |
| 3171 |
|
| 3172 |
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild |
| 3173 |
deleted file mode 100644 |
| 3174 |
index 4b92ca0..0000000 |
| 3175 |
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild |
| 3176 |
+++ /dev/null |
| 3177 |
@@ -1,15 +0,0 @@ |
| 3178 |
-# Copyright 1999-2015 Gentoo Foundation |
| 3179 |
-# Distributed under the terms of the GNU General Public License v2 |
| 3180 |
-# $Header: $ |
| 3181 |
- |
| 3182 |
-EAPI=5 |
| 3183 |
- |
| 3184 |
-EBO_DESCRIPTION="the Phylogeny Inference Package" |
| 3185 |
- |
| 3186 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 3187 |
-AUTOTOOLS_AUTORECONF=1 |
| 3188 |
-inherit emboss-r1 |
| 3189 |
- |
| 3190 |
-LICENSE+=" freedist" |
| 3191 |
- |
| 3192 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 3193 |
|
| 3194 |
diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch |
| 3195 |
deleted file mode 100644 |
| 3196 |
index e0efb74..0000000 |
| 3197 |
--- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch |
| 3198 |
+++ /dev/null |
| 3199 |
@@ -1,98 +0,0 @@ |
| 3200 |
---- PHYLIPNEW-3.69.650/configure.ac |
| 3201 |
-+++ PHYLIPNEW-3.69.650/configure.ac |
| 3202 |
-@@ -635,33 +635,6 @@ |
| 3203 |
- |
| 3204 |
- |
| 3205 |
- |
| 3206 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 3207 |
--dnl to see which version's configure.in these lines come from |
| 3208 |
-- |
| 3209 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 3210 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 3211 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 3212 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 3213 |
--dnl that many releases anyway. |
| 3214 |
-- |
| 3215 |
--PCRE_MAJOR="7" |
| 3216 |
--PCRE_MINOR="9" |
| 3217 |
--PCRE_DATE="11-Apr-2009" |
| 3218 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 3219 |
-- |
| 3220 |
--dnl Default values for miscellaneous macros |
| 3221 |
-- |
| 3222 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 3223 |
-- |
| 3224 |
--dnl Provide versioning information for libtool shared libraries that |
| 3225 |
--dnl are built by default on Unix systems. |
| 3226 |
-- |
| 3227 |
--PCRE_LIB_VERSION="0:1:0" |
| 3228 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 3229 |
-- |
| 3230 |
-- |
| 3231 |
-- |
| 3232 |
-- |
| 3233 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 3234 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 3235 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 3236 |
-@@ -781,21 +754,6 @@ |
| 3237 |
- |
| 3238 |
- |
| 3239 |
- |
| 3240 |
--dnl "Export" these variables for PCRE |
| 3241 |
-- |
| 3242 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 3243 |
--AC_SUBST([HAVE_STRERROR]) |
| 3244 |
--AC_SUBST([PCRE_MAJOR]) |
| 3245 |
--AC_SUBST([PCRE_MINOR]) |
| 3246 |
--AC_SUBST([PCRE_DATE]) |
| 3247 |
--AC_SUBST([PCRE_VERSION]) |
| 3248 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 3249 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 3250 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 3251 |
-- |
| 3252 |
-- |
| 3253 |
-- |
| 3254 |
-- |
| 3255 |
- dnl Test if --enable-localforce given |
| 3256 |
- locallink="no" |
| 3257 |
- embprefix="/usr/local" |
| 3258 |
-@@ -918,6 +876,11 @@ |
| 3259 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 3260 |
- |
| 3261 |
- |
| 3262 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 3263 |
-+[ |
| 3264 |
-+dnl using system libraries |
| 3265 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 3266 |
-+]) |
| 3267 |
- |
| 3268 |
- |
| 3269 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 3270 |
---- PHYLIPNEW-3.69.650/src/Makefile.am |
| 3271 |
-+++ PHYLIPNEW-3.69.650/src/Makefile.am |
| 3272 |
-@@ -16,10 +16,7 @@ |
| 3273 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 3274 |
- -I../../../ajax/acd -I../../../plplot |
| 3275 |
- else |
| 3276 |
--AM_CPPFLAGS = -I../include -I${embprefix}/include \ |
| 3277 |
-- -I${embprefix}/include/eplplot \ |
| 3278 |
-- $(NLINCLUDES) \ |
| 3279 |
-- -I${embprefix}/include/epcre |
| 3280 |
-+AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 3281 |
- endif |
| 3282 |
- |
| 3283 |
- if ISSHARED |
| 3284 |
-@@ -120,5 +117,5 @@ |
| 3285 |
- ../../../plplot/libeplplot.la $(XLIB) |
| 3286 |
- else |
| 3287 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 3288 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 3289 |
-+ -lajax $(NLADD) $(XLIB) |
| 3290 |
- endif |
| 3291 |
---- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am |
| 3292 |
-+++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am |
| 3293 |
-@@ -1,3 +1,3 @@ |
| 3294 |
- |
| 3295 |
--pkgdata_DATA = *.acd |
| 3296 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 3297 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 3298 |
|
| 3299 |
diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml |
| 3300 |
deleted file mode 100644 |
| 3301 |
index f17a827..0000000 |
| 3302 |
--- a/sci-biology/embassy-phylipnew/metadata.xml |
| 3303 |
+++ /dev/null |
| 3304 |
@@ -1,5 +0,0 @@ |
| 3305 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 3306 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 3307 |
-<pkgmetadata> |
| 3308 |
- <herd>sci-biology</herd> |
| 3309 |
-</pkgmetadata> |
| 3310 |
|
| 3311 |
diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog |
| 3312 |
deleted file mode 100644 |
| 3313 |
index 2d33990..0000000 |
| 3314 |
--- a/sci-biology/embassy-signature/ChangeLog |
| 3315 |
+++ /dev/null |
| 3316 |
@@ -1,116 +0,0 @@ |
| 3317 |
-# ChangeLog for sci-biology/embassy-signature |
| 3318 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 3319 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.19 2010/01/01 21:59:44 fauli Exp $ |
| 3320 |
- |
| 3321 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 3322 |
- -embassy-signature-0.1.0-r5.ebuild, embassy-signature-0.1.650.ebuild, |
| 3323 |
- -files/embassy-signature-0.1.0-r5.patch, metadata.xml: |
| 3324 |
- Bump eclass, drop old |
| 3325 |
- |
| 3326 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 3327 |
- embassy-signature-0.1.0-r5.ebuild: |
| 3328 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 3329 |
- |
| 3330 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> |
| 3331 |
- embassy-signature-0.1.0-r5.ebuild, files/embassy-signature-0.1.0-r5.patch: |
| 3332 |
- Fixed for reviewed eclass |
| 3333 |
- |
| 3334 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 3335 |
- embassy-signature-0.1.0-r5.ebuild: |
| 3336 |
- Naming of eclass changed |
| 3337 |
- |
| 3338 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 3339 |
- embassy-signature-0.1.0-r5.ebuild: |
| 3340 |
- EOV not needed to be set anymore |
| 3341 |
- |
| 3342 |
-*embassy-signature-0.1.0-r5 (10 Mar 2011) |
| 3343 |
- |
| 3344 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 3345 |
- +embassy-signature-0.1.0-r5.ebuild, +files/embassy-signature-0.1.0-r5.patch, |
| 3346 |
- +metadata.xml: |
| 3347 |
- Move to new embassy-ng.eclass |
| 3348 |
- |
| 3349 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 3350 |
- embassy-signature-0.1.0-r4.ebuild: |
| 3351 |
- Transfer Prefix keywords |
| 3352 |
- |
| 3353 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 3354 |
- Giving up maintainership of this package. |
| 3355 |
- |
| 3356 |
-*embassy-signature-0.1.0-r4 (01 Sep 2009) |
| 3357 |
- |
| 3358 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3359 |
- +embassy-signature-0.1.0-r4.ebuild: |
| 3360 |
- Updated version for EMBASSY 6.1.0. |
| 3361 |
- |
| 3362 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3363 |
- embassy-signature-0.1.0-r3.ebuild: |
| 3364 |
- Stabilised on amd64 and x86. |
| 3365 |
- |
| 3366 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3367 |
- -embassy-signature-0.1.0-r2.ebuild: |
| 3368 |
- Pruning version that will never be stabilised. |
| 3369 |
- |
| 3370 |
-*embassy-signature-0.1.0-r3 (27 Aug 2008) |
| 3371 |
- |
| 3372 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3373 |
- +embassy-signature-0.1.0-r3.ebuild: |
| 3374 |
- New upstream version/package for EMBASSY 6.0.1. |
| 3375 |
- |
| 3376 |
-*embassy-signature-0.1.0-r2 (18 Jul 2007) |
| 3377 |
- |
| 3378 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 3379 |
- +embassy-signature-0.1.0-r2.ebuild: |
| 3380 |
- New upstream packaging for EMBOSS 5.0.0. |
| 3381 |
- |
| 3382 |
- 16 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 3383 |
- embassy-signature-0.1.0-r1.ebuild: |
| 3384 |
- Added ~amd64. |
| 3385 |
- |
| 3386 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 3387 |
- -embassy-signature-0.1.0.ebuild: |
| 3388 |
- Pruning old version. |
| 3389 |
- |
| 3390 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-signature-0.1.0-r1.ebuild: |
| 3391 |
- Stable on ppc wrt bug 153766 |
| 3392 |
- |
| 3393 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 3394 |
- embassy-signature-0.1.0-r1.ebuild: |
| 3395 |
- Added ~sparc |
| 3396 |
- |
| 3397 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 3398 |
- embassy-signature-0.1.0.ebuild, embassy-signature-0.1.0-r1.ebuild: |
| 3399 |
- Dropped ppc-macos, see you in prefix. |
| 3400 |
- |
| 3401 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 3402 |
- embassy-signature-0.1.0-r1.ebuild: |
| 3403 |
- Added to x86. |
| 3404 |
- |
| 3405 |
-*embassy-signature-0.1.0-r1 (21 Jul 2006) |
| 3406 |
- |
| 3407 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 3408 |
- +embassy-signature-0.1.0-r1.ebuild: |
| 3409 |
- New upstream version building against EMBOSS 4.0.0. |
| 3410 |
- |
| 3411 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 3412 |
- embassy-signature-0.1.0.ebuild: |
| 3413 |
- Fixed download URL (silent upstream repackaging). |
| 3414 |
- |
| 3415 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 3416 |
- embassy-signature-0.1.0.ebuild: |
| 3417 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 3418 |
- |
| 3419 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 3420 |
- embassy-signature-0.1.0.ebuild: |
| 3421 |
- Stable on ppc. |
| 3422 |
- |
| 3423 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 3424 |
- embassy-signature-0.1.0.ebuild: |
| 3425 |
- Added to x86. |
| 3426 |
- |
| 3427 |
-*embassy-signature-0.1.0 (07 Aug 2005) |
| 3428 |
- |
| 3429 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 3430 |
- +embassy-signature-0.1.0.ebuild: |
| 3431 |
- New import. This package is part of the EMBASSY 3.0.0 distribution. |
| 3432 |
- |
| 3433 |
|
| 3434 |
diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild |
| 3435 |
deleted file mode 100644 |
| 3436 |
index 1cfd5aa..0000000 |
| 3437 |
--- a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild |
| 3438 |
+++ /dev/null |
| 3439 |
@@ -1,13 +0,0 @@ |
| 3440 |
-# Copyright 1999-2015 Gentoo Foundation |
| 3441 |
-# Distributed under the terms of the GNU General Public License v2 |
| 3442 |
-# $Header: $ |
| 3443 |
- |
| 3444 |
-EAPI=5 |
| 3445 |
- |
| 3446 |
-EBO_DESCRIPTION="Protein signature add-on package" |
| 3447 |
- |
| 3448 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 3449 |
-AUTOTOOLS_AUTORECONF=1 |
| 3450 |
-inherit emboss-r1 |
| 3451 |
- |
| 3452 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 3453 |
|
| 3454 |
diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch |
| 3455 |
deleted file mode 100644 |
| 3456 |
index 5197c64..0000000 |
| 3457 |
--- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch |
| 3458 |
+++ /dev/null |
| 3459 |
@@ -1,90 +0,0 @@ |
| 3460 |
---- SIGNATURE-0.1.650/configure.ac |
| 3461 |
-+++ SIGNATURE-0.1.650/configure.ac |
| 3462 |
-@@ -635,33 +635,6 @@ |
| 3463 |
- |
| 3464 |
- |
| 3465 |
- |
| 3466 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 3467 |
--dnl to see which version's configure.in these lines come from |
| 3468 |
-- |
| 3469 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 3470 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 3471 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 3472 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 3473 |
--dnl that many releases anyway. |
| 3474 |
-- |
| 3475 |
--PCRE_MAJOR="7" |
| 3476 |
--PCRE_MINOR="9" |
| 3477 |
--PCRE_DATE="11-Apr-2009" |
| 3478 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 3479 |
-- |
| 3480 |
--dnl Default values for miscellaneous macros |
| 3481 |
-- |
| 3482 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 3483 |
-- |
| 3484 |
--dnl Provide versioning information for libtool shared libraries that |
| 3485 |
--dnl are built by default on Unix systems. |
| 3486 |
-- |
| 3487 |
--PCRE_LIB_VERSION="0:1:0" |
| 3488 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 3489 |
-- |
| 3490 |
-- |
| 3491 |
-- |
| 3492 |
-- |
| 3493 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 3494 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 3495 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 3496 |
-@@ -737,21 +710,6 @@ |
| 3497 |
- |
| 3498 |
- |
| 3499 |
- |
| 3500 |
--dnl "Export" these variables for PCRE |
| 3501 |
-- |
| 3502 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 3503 |
--AC_SUBST([HAVE_STRERROR]) |
| 3504 |
--AC_SUBST([PCRE_MAJOR]) |
| 3505 |
--AC_SUBST([PCRE_MINOR]) |
| 3506 |
--AC_SUBST([PCRE_DATE]) |
| 3507 |
--AC_SUBST([PCRE_VERSION]) |
| 3508 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 3509 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 3510 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 3511 |
-- |
| 3512 |
-- |
| 3513 |
-- |
| 3514 |
-- |
| 3515 |
- dnl Test if --enable-localforce given |
| 3516 |
- locallink="no" |
| 3517 |
- embprefix="/usr/local" |
| 3518 |
-@@ -874,6 +832,11 @@ |
| 3519 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 3520 |
- |
| 3521 |
- |
| 3522 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 3523 |
-+[ |
| 3524 |
-+dnl using system libraries |
| 3525 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 3526 |
-+]) |
| 3527 |
- |
| 3528 |
- |
| 3529 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 3530 |
---- SIGNATURE-0.1.650/src/Makefile.am |
| 3531 |
-+++ SIGNATURE-0.1.650/src/Makefile.am |
| 3532 |
-@@ -17,9 +17,7 @@ |
| 3533 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 3534 |
- -I../../../ajax/acd -I../../../plplot |
| 3535 |
- else |
| 3536 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 3537 |
-- $(NLINCLUDES) \ |
| 3538 |
-- -I${embprefix}/include/epcre |
| 3539 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 3540 |
- endif |
| 3541 |
- |
| 3542 |
- if ISSHARED |
| 3543 |
-@@ -68,5 +66,5 @@ |
| 3544 |
- $(XLIB) |
| 3545 |
- else |
| 3546 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 3547 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 3548 |
-+ -lajax $(NLADD) $(XLIB) |
| 3549 |
- endif |
| 3550 |
|
| 3551 |
diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml |
| 3552 |
deleted file mode 100644 |
| 3553 |
index f17a827..0000000 |
| 3554 |
--- a/sci-biology/embassy-signature/metadata.xml |
| 3555 |
+++ /dev/null |
| 3556 |
@@ -1,5 +0,0 @@ |
| 3557 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 3558 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 3559 |
-<pkgmetadata> |
| 3560 |
- <herd>sci-biology</herd> |
| 3561 |
-</pkgmetadata> |
| 3562 |
|
| 3563 |
diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog |
| 3564 |
deleted file mode 100644 |
| 3565 |
index 06ab2b2..0000000 |
| 3566 |
--- a/sci-biology/embassy-structure/ChangeLog |
| 3567 |
+++ /dev/null |
| 3568 |
@@ -1,116 +0,0 @@ |
| 3569 |
-# ChangeLog for sci-biology/embassy-structure |
| 3570 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 3571 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.19 2010/01/01 21:57:51 fauli Exp $ |
| 3572 |
- |
| 3573 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> |
| 3574 |
- -embassy-structure-0.1.0-r5.ebuild, embassy-structure-0.1.650.ebuild, |
| 3575 |
- -files/embassy-structure-0.1.0-r5.patch, metadata.xml: |
| 3576 |
- Bump eclass, drop old |
| 3577 |
- |
| 3578 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> |
| 3579 |
- embassy-structure-0.1.0-r5.ebuild: |
| 3580 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 3581 |
- |
| 3582 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> |
| 3583 |
- embassy-structure-0.1.0-r5.ebuild, files/embassy-structure-0.1.0-r5.patch: |
| 3584 |
- Fixed for reviewed eclass |
| 3585 |
- |
| 3586 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> |
| 3587 |
- embassy-structure-0.1.0-r5.ebuild: |
| 3588 |
- Naming of eclass changed |
| 3589 |
- |
| 3590 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> |
| 3591 |
- embassy-structure-0.1.0-r5.ebuild: |
| 3592 |
- EOV not needed to be set anymore |
| 3593 |
- |
| 3594 |
-*embassy-structure-0.1.0-r5 (10 Mar 2011) |
| 3595 |
- |
| 3596 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> |
| 3597 |
- +embassy-structure-0.1.0-r5.ebuild, +files/embassy-structure-0.1.0-r5.patch, |
| 3598 |
- +metadata.xml: |
| 3599 |
- Move to new embassy-ng.eclass |
| 3600 |
- |
| 3601 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 3602 |
- embassy-structure-0.1.0-r4.ebuild: |
| 3603 |
- Transfer Prefix keywords |
| 3604 |
- |
| 3605 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 3606 |
- Giving up maintainership of this package. |
| 3607 |
- |
| 3608 |
-*embassy-structure-0.1.0-r4 (01 Sep 2009) |
| 3609 |
- |
| 3610 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3611 |
- +embassy-structure-0.1.0-r4.ebuild: |
| 3612 |
- Updated version for EMBASSY 6.1.0. |
| 3613 |
- |
| 3614 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3615 |
- embassy-structure-0.1.0-r3.ebuild: |
| 3616 |
- Stabilised on amd64 and x86. |
| 3617 |
- |
| 3618 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3619 |
- -embassy-structure-0.1.0-r2.ebuild: |
| 3620 |
- Pruning version that will never be stabilised. |
| 3621 |
- |
| 3622 |
-*embassy-structure-0.1.0-r3 (27 Aug 2008) |
| 3623 |
- |
| 3624 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3625 |
- +embassy-structure-0.1.0-r3.ebuild: |
| 3626 |
- New upstream version/package for EMBASSY 6.0.1. |
| 3627 |
- |
| 3628 |
-*embassy-structure-0.1.0-r2 (18 Jul 2007) |
| 3629 |
- |
| 3630 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 3631 |
- +embassy-structure-0.1.0-r2.ebuild: |
| 3632 |
- New upstream packaging for EMBOSS 5.0.0. |
| 3633 |
- |
| 3634 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 3635 |
- embassy-structure-0.1.0-r1.ebuild: |
| 3636 |
- Added ~amd64. |
| 3637 |
- |
| 3638 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 3639 |
- -embassy-structure-0.1.0.ebuild: |
| 3640 |
- Pruning old version. |
| 3641 |
- |
| 3642 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-structure-0.1.0-r1.ebuild: |
| 3643 |
- Stable on ppc wrt bug 153766 |
| 3644 |
- |
| 3645 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 3646 |
- embassy-structure-0.1.0-r1.ebuild: |
| 3647 |
- Added ~sparc |
| 3648 |
- |
| 3649 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 3650 |
- embassy-structure-0.1.0.ebuild, embassy-structure-0.1.0-r1.ebuild: |
| 3651 |
- Dropped ppc-macos, see you in prefix. |
| 3652 |
- |
| 3653 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 3654 |
- embassy-structure-0.1.0-r1.ebuild: |
| 3655 |
- Added to x86. |
| 3656 |
- |
| 3657 |
-*embassy-structure-0.1.0-r1 (21 Jul 2006) |
| 3658 |
- |
| 3659 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 3660 |
- +embassy-structure-0.1.0-r1.ebuild: |
| 3661 |
- New upstream version building against EMBOSS 4.0.0. |
| 3662 |
- |
| 3663 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 3664 |
- embassy-structure-0.1.0.ebuild: |
| 3665 |
- Fixed download URL (silent upstream repackaging). |
| 3666 |
- |
| 3667 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 3668 |
- embassy-structure-0.1.0.ebuild: |
| 3669 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 3670 |
- |
| 3671 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 3672 |
- embassy-structure-0.1.0.ebuild: |
| 3673 |
- Stable on ppc. |
| 3674 |
- |
| 3675 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 3676 |
- embassy-structure-0.1.0.ebuild: |
| 3677 |
- Added to x86. |
| 3678 |
- |
| 3679 |
-*embassy-structure-0.1.0 (07 Aug 2005) |
| 3680 |
- |
| 3681 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 3682 |
- +embassy-structure-0.1.0.ebuild: |
| 3683 |
- New import. This package is part of the EMBASSY 3.0.0 distribution. |
| 3684 |
- |
| 3685 |
|
| 3686 |
diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild |
| 3687 |
deleted file mode 100644 |
| 3688 |
index 377bb48..0000000 |
| 3689 |
--- a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild |
| 3690 |
+++ /dev/null |
| 3691 |
@@ -1,13 +0,0 @@ |
| 3692 |
-# Copyright 1999-2015 Gentoo Foundation |
| 3693 |
-# Distributed under the terms of the GNU General Public License v2 |
| 3694 |
-# $Header: $ |
| 3695 |
- |
| 3696 |
-EAPI=5 |
| 3697 |
- |
| 3698 |
-EBO_DESCRIPTION="Protein structure add-on package" |
| 3699 |
- |
| 3700 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 3701 |
-AUTOTOOLS_AUTORECONF=1 |
| 3702 |
-inherit emboss-r1 |
| 3703 |
- |
| 3704 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 3705 |
|
| 3706 |
diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch |
| 3707 |
deleted file mode 100644 |
| 3708 |
index c87eefd..0000000 |
| 3709 |
--- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch |
| 3710 |
+++ /dev/null |
| 3711 |
@@ -1,90 +0,0 @@ |
| 3712 |
---- STRUCTURE-0.1.650/configure.ac |
| 3713 |
-+++ STRUCTURE-0.1.650/configure.ac |
| 3714 |
-@@ -635,33 +635,6 @@ |
| 3715 |
- |
| 3716 |
- |
| 3717 |
- |
| 3718 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 3719 |
--dnl to see which version's configure.in these lines come from |
| 3720 |
-- |
| 3721 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 3722 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 3723 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 3724 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 3725 |
--dnl that many releases anyway. |
| 3726 |
-- |
| 3727 |
--PCRE_MAJOR="7" |
| 3728 |
--PCRE_MINOR="9" |
| 3729 |
--PCRE_DATE="11-Apr-2009" |
| 3730 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 3731 |
-- |
| 3732 |
--dnl Default values for miscellaneous macros |
| 3733 |
-- |
| 3734 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 3735 |
-- |
| 3736 |
--dnl Provide versioning information for libtool shared libraries that |
| 3737 |
--dnl are built by default on Unix systems. |
| 3738 |
-- |
| 3739 |
--PCRE_LIB_VERSION="0:1:0" |
| 3740 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 3741 |
-- |
| 3742 |
-- |
| 3743 |
-- |
| 3744 |
-- |
| 3745 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 3746 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 3747 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 3748 |
-@@ -737,21 +710,6 @@ |
| 3749 |
- |
| 3750 |
- |
| 3751 |
- |
| 3752 |
--dnl "Export" these variables for PCRE |
| 3753 |
-- |
| 3754 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 3755 |
--AC_SUBST([HAVE_STRERROR]) |
| 3756 |
--AC_SUBST([PCRE_MAJOR]) |
| 3757 |
--AC_SUBST([PCRE_MINOR]) |
| 3758 |
--AC_SUBST([PCRE_DATE]) |
| 3759 |
--AC_SUBST([PCRE_VERSION]) |
| 3760 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 3761 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 3762 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 3763 |
-- |
| 3764 |
-- |
| 3765 |
-- |
| 3766 |
-- |
| 3767 |
- dnl Test if --enable-localforce given |
| 3768 |
- locallink="no" |
| 3769 |
- embprefix="/usr/local" |
| 3770 |
-@@ -874,6 +832,11 @@ |
| 3771 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 3772 |
- |
| 3773 |
- |
| 3774 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 3775 |
-+[ |
| 3776 |
-+dnl using system libraries |
| 3777 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 3778 |
-+]) |
| 3779 |
- |
| 3780 |
- |
| 3781 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 3782 |
---- STRUCTURE-0.1.650/src/Makefile.am |
| 3783 |
-+++ STRUCTURE-0.1.650/src/Makefile.am |
| 3784 |
-@@ -17,9 +17,7 @@ |
| 3785 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 3786 |
- -I../../../ajax/acd -I../../../plplot |
| 3787 |
- else |
| 3788 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 3789 |
-- $(NLINCLUDES) \ |
| 3790 |
-- -I${embprefix}/include/epcre |
| 3791 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 3792 |
- endif |
| 3793 |
- |
| 3794 |
- if ISSHARED |
| 3795 |
-@@ -66,5 +64,5 @@ |
| 3796 |
- $(XLIB) |
| 3797 |
- else |
| 3798 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 3799 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 3800 |
-+ -lajax $(NLADD) $(XLIB) |
| 3801 |
- endif |
| 3802 |
|
| 3803 |
diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml |
| 3804 |
deleted file mode 100644 |
| 3805 |
index f17a827..0000000 |
| 3806 |
--- a/sci-biology/embassy-structure/metadata.xml |
| 3807 |
+++ /dev/null |
| 3808 |
@@ -1,5 +0,0 @@ |
| 3809 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 3810 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 3811 |
-<pkgmetadata> |
| 3812 |
- <herd>sci-biology</herd> |
| 3813 |
-</pkgmetadata> |
| 3814 |
|
| 3815 |
diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog |
| 3816 |
deleted file mode 100644 |
| 3817 |
index 0bc8739..0000000 |
| 3818 |
--- a/sci-biology/embassy-topo/ChangeLog |
| 3819 |
+++ /dev/null |
| 3820 |
@@ -1,161 +0,0 @@ |
| 3821 |
-# ChangeLog for sci-biology/embassy-topo |
| 3822 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 3823 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.29 2010/01/01 21:54:52 fauli Exp $ |
| 3824 |
- |
| 3825 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-topo-2.0.0.ebuild, |
| 3826 |
- embassy-topo-2.0.650.ebuild, -files/embassy-topo-2.0.0.patch, metadata.xml: |
| 3827 |
- Bump eclass, drop old |
| 3828 |
- |
| 3829 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-topo-2.0.0.ebuild: |
| 3830 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 3831 |
- |
| 3832 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-topo-2.0.0.ebuild, |
| 3833 |
- files/embassy-topo-2.0.0.patch: |
| 3834 |
- Fixed for reviewed eclass |
| 3835 |
- |
| 3836 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-topo-2.0.0.ebuild: |
| 3837 |
- Naming of eclass changed |
| 3838 |
- |
| 3839 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-topo-2.0.0.ebuild: |
| 3840 |
- EOV not needed to be set anymore |
| 3841 |
- |
| 3842 |
-*embassy-topo-2.0.0 (10 Mar 2011) |
| 3843 |
- |
| 3844 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-topo-2.0.0.ebuild, |
| 3845 |
- +files/embassy-topo-2.0.0.patch, +metadata.xml: |
| 3846 |
- Move to new embassy-ng.eclass |
| 3847 |
- |
| 3848 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 3849 |
- embassy-topo-1.0.0-r6.ebuild: |
| 3850 |
- Transfer Prefix keywords |
| 3851 |
- |
| 3852 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 3853 |
- Giving up maintainership of this package. |
| 3854 |
- |
| 3855 |
-*embassy-topo-1.0.0-r6 (01 Sep 2009) |
| 3856 |
- |
| 3857 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3858 |
- +embassy-topo-1.0.0-r6.ebuild: |
| 3859 |
- Updated version for EMBASSY 6.1.0. |
| 3860 |
- |
| 3861 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 3862 |
- embassy-topo-1.0.0-r5.ebuild: |
| 3863 |
- Stabilised on amd64 and x86. |
| 3864 |
- |
| 3865 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3866 |
- -embassy-topo-1.0.0-r4.ebuild: |
| 3867 |
- Pruning version that will never be stabilised. |
| 3868 |
- |
| 3869 |
-*embassy-topo-1.0.0-r5 (27 Aug 2008) |
| 3870 |
- |
| 3871 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 3872 |
- +embassy-topo-1.0.0-r5.ebuild: |
| 3873 |
- New upstream version/package for EMBASSY 6.0.1. |
| 3874 |
- |
| 3875 |
-*embassy-topo-1.0.0-r4 (18 Jul 2007) |
| 3876 |
- |
| 3877 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 3878 |
- +embassy-topo-1.0.0-r4.ebuild: |
| 3879 |
- New upstream packaging for EMBOSS 5.0.0. |
| 3880 |
- |
| 3881 |
- 15 Feb 2007; Jeff Gardner <je_fro@g.o> |
| 3882 |
- embassy-topo-1.0.0-r3.ebuild: |
| 3883 |
- Adding ~amd64 |
| 3884 |
- |
| 3885 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 3886 |
- -embassy-topo-1.0.0-r2.ebuild: |
| 3887 |
- Pruning old version. |
| 3888 |
- |
| 3889 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-topo-1.0.0-r3.ebuild: |
| 3890 |
- Stable on ppc wrt bug 153766 |
| 3891 |
- |
| 3892 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> |
| 3893 |
- embassy-topo-1.0.0-r3.ebuild: |
| 3894 |
- Marked ~sparc |
| 3895 |
- |
| 3896 |
- 02 Nov 2006; Fabian Groffen <grobian@g.o> |
| 3897 |
- embassy-topo-1.0.0-r2.ebuild, embassy-topo-1.0.0-r3.ebuild: |
| 3898 |
- Dropped ppc-macos, see you in prefix. |
| 3899 |
- |
| 3900 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> |
| 3901 |
- embassy-topo-1.0.0-r3.ebuild: |
| 3902 |
- Added to x86. |
| 3903 |
- |
| 3904 |
-*embassy-topo-1.0.0-r3 (21 Jul 2006) |
| 3905 |
- |
| 3906 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 3907 |
- +embassy-topo-1.0.0-r3.ebuild: |
| 3908 |
- New upstream version building against EMBOSS 4.0.0. |
| 3909 |
- |
| 3910 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> |
| 3911 |
- embassy-topo-1.0.0-r2.ebuild: |
| 3912 |
- Fixed download URL (silent upstream repackaging). |
| 3913 |
- |
| 3914 |
- 04 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 3915 |
- -embassy-topo-1.0.0-r1.ebuild: |
| 3916 |
- Removed obsolete version. |
| 3917 |
- |
| 3918 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> |
| 3919 |
- embassy-topo-1.0.0-r2.ebuild: |
| 3920 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 3921 |
- |
| 3922 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> |
| 3923 |
- embassy-topo-1.0.0-r2.ebuild: |
| 3924 |
- Stable on ppc. |
| 3925 |
- |
| 3926 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> |
| 3927 |
- embassy-topo-1.0.0-r2.ebuild: |
| 3928 |
- Added to x86. |
| 3929 |
- |
| 3930 |
-*embassy-topo-1.0.0-r2 (07 Aug 2005) |
| 3931 |
- |
| 3932 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> |
| 3933 |
- embassy-topo-1.0.0-r1.ebuild, +embassy-topo-1.0.0-r2.ebuild: |
| 3934 |
- Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of |
| 3935 |
- EMBASSY 3.0.0. |
| 3936 |
- |
| 3937 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> |
| 3938 |
- -embassy-topo-1.0.0.ebuild: |
| 3939 |
- Removed old version. |
| 3940 |
- |
| 3941 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> |
| 3942 |
- embassy-topo-1.0.0-r1.ebuild: |
| 3943 |
- Stable ppc-macos Bug 96819 |
| 3944 |
- |
| 3945 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> |
| 3946 |
- embassy-topo-1.0.0-r1.ebuild: |
| 3947 |
- Marked ppc stable. |
| 3948 |
- |
| 3949 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> |
| 3950 |
- embassy-topo-1.0.0-r1.ebuild: |
| 3951 |
- Added to x86. |
| 3952 |
- |
| 3953 |
-*embassy-topo-1.0.0-r1 (25 Mar 2005) |
| 3954 |
- |
| 3955 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> |
| 3956 |
- +embassy-topo-1.0.0-r1.ebuild: |
| 3957 |
- Build against the EMBOSS 2.10 source tree. |
| 3958 |
- |
| 3959 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> embassy-topo-1.0.0.ebuild: |
| 3960 |
- Stable ppc-macos |
| 3961 |
- |
| 3962 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-topo-1.0.0.ebuild: |
| 3963 |
- Unstable ppc-macos |
| 3964 |
- |
| 3965 |
-*embassy-topo-1.0.0 (23 Dec 2004) |
| 3966 |
- |
| 3967 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 3968 |
- +embassy-topo-1.0.0.ebuild: |
| 3969 |
- Moved from app-sci/embassy-topo to sci-biology/embassy-topo. |
| 3970 |
- |
| 3971 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> embassy-topo-1.0.0.ebuild: |
| 3972 |
- Added to x86. |
| 3973 |
- |
| 3974 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-topo-1.0.0.ebuild: |
| 3975 |
- Added to ~ppc. |
| 3976 |
- |
| 3977 |
-* embassy-topo-1.0.0 (19 Jul 2004) |
| 3978 |
- |
| 3979 |
- 19 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 3980 |
- embassy-topo-1.0.0.ebuild, metadata.xml, ChangeLog |
| 3981 |
- Initial import. |
| 3982 |
|
| 3983 |
diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild |
| 3984 |
deleted file mode 100644 |
| 3985 |
index 8e8eb56..0000000 |
| 3986 |
--- a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild |
| 3987 |
+++ /dev/null |
| 3988 |
@@ -1,13 +0,0 @@ |
| 3989 |
-# Copyright 1999-2015 Gentoo Foundation |
| 3990 |
-# Distributed under the terms of the GNU General Public License v2 |
| 3991 |
-# $Header: $ |
| 3992 |
- |
| 3993 |
-EAPI=5 |
| 3994 |
- |
| 3995 |
-EBO_DESCRIPTION="Transmembrane protein display" |
| 3996 |
- |
| 3997 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 3998 |
-AUTOTOOLS_AUTORECONF=1 |
| 3999 |
-inherit emboss-r1 |
| 4000 |
- |
| 4001 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
| 4002 |
|
| 4003 |
diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch |
| 4004 |
deleted file mode 100644 |
| 4005 |
index 7ddda05..0000000 |
| 4006 |
--- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch |
| 4007 |
+++ /dev/null |
| 4008 |
@@ -1,97 +0,0 @@ |
| 4009 |
---- TOPO-2.0.650/configure.ac |
| 4010 |
-+++ TOPO-2.0.650/configure.ac |
| 4011 |
-@@ -635,33 +635,6 @@ |
| 4012 |
- |
| 4013 |
- |
| 4014 |
- |
| 4015 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 4016 |
--dnl to see which version's configure.in these lines come from |
| 4017 |
-- |
| 4018 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 4019 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 4020 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 4021 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 4022 |
--dnl that many releases anyway. |
| 4023 |
-- |
| 4024 |
--PCRE_MAJOR="7" |
| 4025 |
--PCRE_MINOR="9" |
| 4026 |
--PCRE_DATE="11-Apr-2009" |
| 4027 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 4028 |
-- |
| 4029 |
--dnl Default values for miscellaneous macros |
| 4030 |
-- |
| 4031 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 4032 |
-- |
| 4033 |
--dnl Provide versioning information for libtool shared libraries that |
| 4034 |
--dnl are built by default on Unix systems. |
| 4035 |
-- |
| 4036 |
--PCRE_LIB_VERSION="0:1:0" |
| 4037 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 4038 |
-- |
| 4039 |
-- |
| 4040 |
-- |
| 4041 |
-- |
| 4042 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 4043 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 4044 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 4045 |
-@@ -737,21 +710,6 @@ |
| 4046 |
- |
| 4047 |
- |
| 4048 |
- |
| 4049 |
--dnl "Export" these variables for PCRE |
| 4050 |
-- |
| 4051 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 4052 |
--AC_SUBST([HAVE_STRERROR]) |
| 4053 |
--AC_SUBST([PCRE_MAJOR]) |
| 4054 |
--AC_SUBST([PCRE_MINOR]) |
| 4055 |
--AC_SUBST([PCRE_DATE]) |
| 4056 |
--AC_SUBST([PCRE_VERSION]) |
| 4057 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 4058 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 4059 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 4060 |
-- |
| 4061 |
-- |
| 4062 |
-- |
| 4063 |
-- |
| 4064 |
- dnl Test if --enable-localforce given |
| 4065 |
- locallink="no" |
| 4066 |
- embprefix="/usr/local" |
| 4067 |
-@@ -874,6 +832,11 @@ |
| 4068 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 4069 |
- |
| 4070 |
- |
| 4071 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 4072 |
-+[ |
| 4073 |
-+dnl using system libraries |
| 4074 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 4075 |
-+]) |
| 4076 |
- |
| 4077 |
- |
| 4078 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 4079 |
---- TOPO-2.0.650/src/Makefile.am |
| 4080 |
-+++ TOPO-2.0.650/src/Makefile.am |
| 4081 |
-@@ -17,9 +17,7 @@ |
| 4082 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 4083 |
- -I../../../ajax/acd -I../../../plplot |
| 4084 |
- else |
| 4085 |
--AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 4086 |
-- $(NLINCLUDES) \ |
| 4087 |
-- -I${embprefix}/include/epcre |
| 4088 |
-+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 4089 |
- endif |
| 4090 |
- |
| 4091 |
- if ISSHARED |
| 4092 |
-@@ -60,5 +58,5 @@ |
| 4093 |
- $(XLIB) |
| 4094 |
- else |
| 4095 |
- LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ |
| 4096 |
-- -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 4097 |
-+ -lajax $(NLADD) $(XLIB) |
| 4098 |
- endif |
| 4099 |
---- TOPO-2.0.650/emboss_acd/Makefile.am |
| 4100 |
-+++ TOPO-2.0.650/emboss_acd/Makefile.am |
| 4101 |
-@@ -1,3 +1,3 @@ |
| 4102 |
- |
| 4103 |
--pkgdata_DATA = *.acd |
| 4104 |
-+pkgdata_DATA = $(srcdir)/*.acd |
| 4105 |
- pkgdatadir=$(prefix)/share/EMBOSS/acd |
| 4106 |
|
| 4107 |
diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml |
| 4108 |
deleted file mode 100644 |
| 4109 |
index f17a827..0000000 |
| 4110 |
--- a/sci-biology/embassy-topo/metadata.xml |
| 4111 |
+++ /dev/null |
| 4112 |
@@ -1,5 +0,0 @@ |
| 4113 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 4114 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 4115 |
-<pkgmetadata> |
| 4116 |
- <herd>sci-biology</herd> |
| 4117 |
-</pkgmetadata> |
| 4118 |
|
| 4119 |
diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog |
| 4120 |
deleted file mode 100644 |
| 4121 |
index 1000b17..0000000 |
| 4122 |
--- a/sci-biology/embassy-vienna/ChangeLog |
| 4123 |
+++ /dev/null |
| 4124 |
@@ -1,65 +0,0 @@ |
| 4125 |
-# ChangeLog for sci-biology/embassy-vienna |
| 4126 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 4127 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.8 2010/01/15 22:47:16 fauli Exp $ |
| 4128 |
- |
| 4129 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-vienna-1.7.2-r2.ebuild, |
| 4130 |
- embassy-vienna-1.7.2.650.ebuild, -files/embassy-vienna-1.7.2-r2.patch, |
| 4131 |
- metadata.xml: |
| 4132 |
- Bump eclass, drop old |
| 4133 |
- |
| 4134 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-vienna-1.7.2-r2.ebuild: |
| 4135 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 4136 |
- |
| 4137 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-vienna-1.7.2-r2.ebuild, |
| 4138 |
- files/embassy-vienna-1.7.2-r2.patch: |
| 4139 |
- Fixed for reviewed eclass |
| 4140 |
- |
| 4141 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-vienna-1.7.2-r2.ebuild: |
| 4142 |
- Naming of eclass changed |
| 4143 |
- |
| 4144 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> embassy-vienna-1.7.2-r2.ebuild: |
| 4145 |
- EOV not needed to be set anymore |
| 4146 |
- |
| 4147 |
-*embassy-vienna-1.7.2-r2 (10 Mar 2011) |
| 4148 |
- |
| 4149 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-vienna-1.7.2-r2.ebuild, |
| 4150 |
- +files/embassy-vienna-1.7.2-r2.patch, +metadata.xml: |
| 4151 |
- Version Bump, Move to new embassy-ng.eclass |
| 4152 |
- |
| 4153 |
- 15 Jan 2010; Christian Faulhammer <fauli@g.o> |
| 4154 |
- embassy-vienna-1.7.2-r1.ebuild: |
| 4155 |
- Transfer Prefix keywords |
| 4156 |
- |
| 4157 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 4158 |
- Giving up maintainership of this package. |
| 4159 |
- |
| 4160 |
-*embassy-vienna-1.7.2-r1 (01 Sep 2009) |
| 4161 |
- |
| 4162 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 4163 |
- +embassy-vienna-1.7.2-r1.ebuild: |
| 4164 |
- Updated version for EMBASSY 6.1.0. |
| 4165 |
- |
| 4166 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> |
| 4167 |
- embassy-vienna-1.7.2.ebuild: |
| 4168 |
- Stabilised on amd64 and x86. |
| 4169 |
- |
| 4170 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 4171 |
- -embassy-vienna-1.6.ebuild: |
| 4172 |
- Pruning version that will never be stabilised. |
| 4173 |
- |
| 4174 |
-*embassy-vienna-1.7.2 (27 Aug 2008) |
| 4175 |
- |
| 4176 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 4177 |
- +embassy-vienna-1.7.2.ebuild: |
| 4178 |
- New upstream version/package for EMBASSY 6.0.1. |
| 4179 |
- |
| 4180 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> |
| 4181 |
- embassy-vienna-1.6.ebuild: |
| 4182 |
- Fixed description. |
| 4183 |
- |
| 4184 |
-*embassy-vienna-1.6 (18 Jul 2007) |
| 4185 |
- |
| 4186 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 4187 |
- +embassy-vienna-1.6.ebuild: |
| 4188 |
- Initial import. |
| 4189 |
- |
| 4190 |
|
| 4191 |
diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild |
| 4192 |
deleted file mode 100644 |
| 4193 |
index 87c5576..0000000 |
| 4194 |
--- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild |
| 4195 |
+++ /dev/null |
| 4196 |
@@ -1,13 +0,0 @@ |
| 4197 |
-# Copyright 1999-2015 Gentoo Foundation |
| 4198 |
-# Distributed under the terms of the GNU General Public License v2 |
| 4199 |
-# $Header: $ |
| 4200 |
- |
| 4201 |
-EAPI=5 |
| 4202 |
- |
| 4203 |
-EBO_DESCRIPTION="Vienna RNA package - RNA folding" |
| 4204 |
- |
| 4205 |
-PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) |
| 4206 |
-AUTOTOOLS_AUTORECONF=1 |
| 4207 |
-inherit emboss-r1 |
| 4208 |
- |
| 4209 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
| 4210 |
|
| 4211 |
diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch |
| 4212 |
deleted file mode 100644 |
| 4213 |
index c9ece69..0000000 |
| 4214 |
--- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch |
| 4215 |
+++ /dev/null |
| 4216 |
@@ -1,98 +0,0 @@ |
| 4217 |
---- VIENNA-1.7.2.650/configure.ac |
| 4218 |
-+++ VIENNA-1.7.2.650/configure.ac |
| 4219 |
-@@ -649,33 +649,6 @@ |
| 4220 |
- |
| 4221 |
- |
| 4222 |
- |
| 4223 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 4224 |
--dnl to see which version's configure.in these lines come from |
| 4225 |
-- |
| 4226 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 4227 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 4228 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 4229 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 4230 |
--dnl that many releases anyway. |
| 4231 |
-- |
| 4232 |
--PCRE_MAJOR="7" |
| 4233 |
--PCRE_MINOR="9" |
| 4234 |
--PCRE_DATE="11-Apr-2009" |
| 4235 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 4236 |
-- |
| 4237 |
--dnl Default values for miscellaneous macros |
| 4238 |
-- |
| 4239 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 4240 |
-- |
| 4241 |
--dnl Provide versioning information for libtool shared libraries that |
| 4242 |
--dnl are built by default on Unix systems. |
| 4243 |
-- |
| 4244 |
--PCRE_LIB_VERSION="0:1:0" |
| 4245 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 4246 |
-- |
| 4247 |
-- |
| 4248 |
-- |
| 4249 |
-- |
| 4250 |
- dnl FIXME: This does no longer seem required with Autoconf 2.67? |
| 4251 |
- dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
| 4252 |
- dnl AS_IF([test "x${with_x}" != "xno"], |
| 4253 |
-@@ -751,21 +724,6 @@ |
| 4254 |
- |
| 4255 |
- |
| 4256 |
- |
| 4257 |
--dnl "Export" these variables for PCRE |
| 4258 |
-- |
| 4259 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 4260 |
--AC_SUBST([HAVE_STRERROR]) |
| 4261 |
--AC_SUBST([PCRE_MAJOR]) |
| 4262 |
--AC_SUBST([PCRE_MINOR]) |
| 4263 |
--AC_SUBST([PCRE_DATE]) |
| 4264 |
--AC_SUBST([PCRE_VERSION]) |
| 4265 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 4266 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 4267 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 4268 |
-- |
| 4269 |
-- |
| 4270 |
-- |
| 4271 |
-- |
| 4272 |
- dnl Test if --enable-localforce given |
| 4273 |
- locallink="no" |
| 4274 |
- embprefix="/usr/local" |
| 4275 |
-@@ -888,6 +846,11 @@ |
| 4276 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 4277 |
- |
| 4278 |
- |
| 4279 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 4280 |
-+[ |
| 4281 |
-+dnl using system libraries |
| 4282 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 4283 |
-+]) |
| 4284 |
- |
| 4285 |
- |
| 4286 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 4287 |
---- VIENNA-1.7.2.650/src/Makefile.am |
| 4288 |
-+++ VIENNA-1.7.2.650/src/Makefile.am |
| 4289 |
-@@ -32,9 +32,7 @@ |
| 4290 |
- -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
| 4291 |
- -I../../../ajax/acd -I../../../plplot |
| 4292 |
- else |
| 4293 |
--AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ |
| 4294 |
-- $(NLINCLUDES) \ |
| 4295 |
-- -I${embprefix}/include/epcre |
| 4296 |
-+AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) |
| 4297 |
- endif |
| 4298 |
- |
| 4299 |
- if ISSHARED |
| 4300 |
-@@ -87,6 +85,7 @@ |
| 4301 |
- endif |
| 4302 |
- |
| 4303 |
- liboviennarna_la_LDFLAGS = $(LINKFLAGS) |
| 4304 |
-+liboviennarna_la_LIBADD = -lajax |
| 4305 |
- |
| 4306 |
- ovrnaalifold_SOURCES = vrnaalifold.c |
| 4307 |
- ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c |
| 4308 |
-@@ -119,5 +118,5 @@ |
| 4309 |
- $(XLIB) |
| 4310 |
- else |
| 4311 |
- LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ |
| 4312 |
-- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
| 4313 |
-+ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) |
| 4314 |
- endif |
| 4315 |
|
| 4316 |
diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml |
| 4317 |
deleted file mode 100644 |
| 4318 |
index f17a827..0000000 |
| 4319 |
--- a/sci-biology/embassy-vienna/metadata.xml |
| 4320 |
+++ /dev/null |
| 4321 |
@@ -1,5 +0,0 @@ |
| 4322 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 4323 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 4324 |
-<pkgmetadata> |
| 4325 |
- <herd>sci-biology</herd> |
| 4326 |
-</pkgmetadata> |
| 4327 |
|
| 4328 |
diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog |
| 4329 |
deleted file mode 100644 |
| 4330 |
index 8f07f9f..0000000 |
| 4331 |
--- a/sci-biology/embassy/ChangeLog |
| 4332 |
+++ /dev/null |
| 4333 |
@@ -1,160 +0,0 @@ |
| 4334 |
-# ChangeLog for sci-biology/embassy |
| 4335 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 4336 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.33 2010/01/01 21:35:29 fauli Exp $ |
| 4337 |
- |
| 4338 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -embassy-6.3.1.ebuild, |
| 4339 |
- metadata.xml: |
| 4340 |
- Drop old |
| 4341 |
- |
| 4342 |
- 25 Jun 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4343 |
- Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 |
| 4344 |
- |
| 4345 |
- 21 Mar 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4346 |
- Fixed for reviewed eclass |
| 4347 |
- |
| 4348 |
- 21 Mar 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4349 |
- Fixed for reviewed eclass |
| 4350 |
- |
| 4351 |
- 20 Mar 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4352 |
- Fixed for reviewed eclass |
| 4353 |
- |
| 4354 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4355 |
- Naming of eclass changed |
| 4356 |
- |
| 4357 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4358 |
- Unset DOCS as we do not have any |
| 4359 |
- |
| 4360 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> embassy-6.3.1.ebuild: |
| 4361 |
- Unset DOCS as we do not have any |
| 4362 |
- |
| 4363 |
-*embassy-6.3.1 (10 Mar 2011) |
| 4364 |
- |
| 4365 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> +embassy-6.3.1.ebuild, |
| 4366 |
- +metadata.xml: |
| 4367 |
- Move to new embassy-ng.eclass |
| 4368 |
- |
| 4369 |
- 01 Jan 2010; Christian Faulhammer <fauli@g.o> embassy-6.1.0.ebuild: |
| 4370 |
- Transfer Prefix keywords |
| 4371 |
- |
| 4372 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 4373 |
- Giving up maintainership of this package. |
| 4374 |
- |
| 4375 |
-*embassy-6.1.0 (01 Sep 2009) |
| 4376 |
- |
| 4377 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> +embassy-6.1.0.ebuild: |
| 4378 |
- New meta-package for EMBASSY packages building against EMBOSS 6.1.0. |
| 4379 |
- |
| 4380 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> embassy-6.0.1.ebuild: |
| 4381 |
- Stabilised on amd64 and x86. |
| 4382 |
- |
| 4383 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> -embassy-5.0.0.ebuild: |
| 4384 |
- Pruning version that will never be stabilised. |
| 4385 |
- |
| 4386 |
-*embassy-6.0.1 (27 Aug 2008) |
| 4387 |
- |
| 4388 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> +embassy-6.0.1.ebuild: |
| 4389 |
- New meta-package for EMBASSY packages building against EMBOSS 6.0.1. |
| 4390 |
- |
| 4391 |
-*embassy-5.0.0 (18 Jul 2007) |
| 4392 |
- |
| 4393 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> +embassy-5.0.0.ebuild: |
| 4394 |
- New meta-package for EMBASSY packages building against EMBOSS 5.0.0. |
| 4395 |
- |
| 4396 |
- 17 Feb 2007; Olivier Fisette <ribosome@g.o> embassy-4.0.0.ebuild: |
| 4397 |
- Added to ~amd64. |
| 4398 |
- |
| 4399 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> -embassy-3.0.0.ebuild: |
| 4400 |
- Pruning old version. |
| 4401 |
- |
| 4402 |
- 03 Nov 2006; nixnut <nixnut@g.o> embassy-4.0.0.ebuild: |
| 4403 |
- Stable on ppc wrt bug 153766 |
| 4404 |
- |
| 4405 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> embassy-4.0.0.ebuild: |
| 4406 |
- Added ~sparc |
| 4407 |
- |
| 4408 |
- 03 Nov 2006; Fabian Groffen <grobian@g.o> embassy-3.0.0.ebuild, |
| 4409 |
- embassy-4.0.0.ebuild: |
| 4410 |
- Dropped ppc-macos, see you in prefix. |
| 4411 |
- |
| 4412 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> embassy-4.0.0.ebuild: |
| 4413 |
- Added to x86. |
| 4414 |
- |
| 4415 |
-*embassy-4.0.0 (21 Jul 2006) |
| 4416 |
- |
| 4417 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> +embassy-4.0.0.ebuild: |
| 4418 |
- New meta-package for EMBASSY packages building against EMBOSS 4.0.0. |
| 4419 |
- |
| 4420 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> -embassy-2.10.0.ebuild: |
| 4421 |
- Removed obsolete version. |
| 4422 |
- |
| 4423 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> embassy-3.0.0.ebuild: |
| 4424 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 4425 |
- |
| 4426 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> embassy-3.0.0.ebuild: |
| 4427 |
- Stable on ppc. |
| 4428 |
- |
| 4429 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> embassy-3.0.0.ebuild: |
| 4430 |
- Added to x86. |
| 4431 |
- |
| 4432 |
-*embassy-3.0.0 (07 Aug 2005) |
| 4433 |
- |
| 4434 |
- 07 Aug 2005; Olivier Fisette <ribosome@g.o> +embassy-3.0.0.ebuild: |
| 4435 |
- New version. This meta-package is for EMBASSY software distributed with |
| 4436 |
- EMBOSS 3.0.0. |
| 4437 |
- |
| 4438 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> -embassy-2.9.0.ebuild: |
| 4439 |
- Removed old version. |
| 4440 |
- |
| 4441 |
- 27 Jul 2005; Lina Pezzella <j4rg0n@g.o> embassy-2.10.0.ebuild: |
| 4442 |
- Stable ppc-macos |
| 4443 |
- |
| 4444 |
- 26 Jun 2005; Lina Pezzella <j4rg0n@g.o> embassy-2.10.0.ebuild: |
| 4445 |
- Testing ppc-macos due to embassy-construct being testing. |
| 4446 |
- |
| 4447 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> embassy-2.10.0.ebuild: |
| 4448 |
- Marked ppc stable. |
| 4449 |
- |
| 4450 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> embassy-2.10.0.ebuild: |
| 4451 |
- Added to x86. |
| 4452 |
- |
| 4453 |
- 06 May 2005; David Holm <dholm@g.o> embassy-2.10.0.ebuild: |
| 4454 |
- Added to ~ppc. |
| 4455 |
- |
| 4456 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> embassy-2.10.0.ebuild: |
| 4457 |
- Added patched versions of DOMAINATRIX and EMNU that work with EMBOSS 2.10. |
| 4458 |
- |
| 4459 |
-*embassy-2.10.0 (25 Mar 2005) |
| 4460 |
- |
| 4461 |
- 25 Mar 2005; Olivier Fisette <ribosome@g.o> embassy-2.9.0.ebuild, |
| 4462 |
- +embassy-2.10.0.ebuild: |
| 4463 |
- Ebuilds for the 2.9 and 2.10 branches of EMBOSS. |
| 4464 |
- |
| 4465 |
- 23 Mar 2005; Olivier Fisette <ribosome@g.o> embassy-2.9.0.ebuild: |
| 4466 |
- EMBOSS 2.10 is incompatible with EMBASSY 2.9 packages. |
| 4467 |
- |
| 4468 |
- 02 Mar 2005; Lina Pezzella <j4rg0n@g.o> embassy-2.9.0.ebuild: |
| 4469 |
- Stable ppc-macos |
| 4470 |
- |
| 4471 |
- 25 Jan 2005; Lina Pezzella <j4rg0n@g.o> embassy-2.9.0.ebuild: |
| 4472 |
- Unstable ppc-macos |
| 4473 |
- |
| 4474 |
-*embassy-2.9.0 (23 Dec 2004) |
| 4475 |
- |
| 4476 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 4477 |
- +embassy-2.9.0.ebuild: |
| 4478 |
- Moved from app-sci/embassy to sci-biology/embassy. |
| 4479 |
- |
| 4480 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> embassy-2.9.0.ebuild: |
| 4481 |
- Added to x86. |
| 4482 |
- |
| 4483 |
- 04 Sep 2004; Thomas Matthijs <axxo@g.o> embassy-2.9.0.ebuild: |
| 4484 |
- fix depend syntax 58347 |
| 4485 |
- |
| 4486 |
- 21 Jul 2004; David Holm <dholm@g.o> embassy-2.9.0.ebuild: |
| 4487 |
- Added to ~ppc. |
| 4488 |
- |
| 4489 |
-* embassy-2.9.0 (19 Jul 2004) |
| 4490 |
- |
| 4491 |
- 19 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 4492 |
- embassy-2.9.0.ebuild, metadata.xml, ChangeLog |
| 4493 |
- Initial import. |
| 4494 |
|
| 4495 |
diff --git a/sci-biology/embassy/embassy-6.6.0.ebuild b/sci-biology/embassy/embassy-6.6.0.ebuild |
| 4496 |
deleted file mode 100644 |
| 4497 |
index 2d1d959..0000000 |
| 4498 |
--- a/sci-biology/embassy/embassy-6.6.0.ebuild |
| 4499 |
+++ /dev/null |
| 4500 |
@@ -1,30 +0,0 @@ |
| 4501 |
-# Copyright 1999-2015 Gentoo Foundation |
| 4502 |
-# Distributed under the terms of the GNU General Public License v2 |
| 4503 |
-# $Header: $ |
| 4504 |
- |
| 4505 |
-EAPI=5 |
| 4506 |
- |
| 4507 |
-DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" |
| 4508 |
-HOMEPAGE="http://emboss.sourceforge.net/embassy/" |
| 4509 |
- |
| 4510 |
-LICENSE+=" freedist" |
| 4511 |
-SLOT="0" |
| 4512 |
-KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" |
| 4513 |
- |
| 4514 |
-RDEPEND+=" |
| 4515 |
- >=sci-biology/embassy-cbstools-1.0.0.650 |
| 4516 |
- >=sci-biology/embassy-clustalomega-1.1.0 |
| 4517 |
- >=sci-biology/embassy-domainatrix-0.1.650 |
| 4518 |
- >=sci-biology/embassy-domalign-0.1.650 |
| 4519 |
- >=sci-biology/embassy-domsearch-0.1.650 |
| 4520 |
- >=sci-biology/embassy-emnu-1.05.650 |
| 4521 |
- >=sci-biology/embassy-esim4-1.0.0.650 |
| 4522 |
- >=sci-biology/embassy-hmmer-2.3.2.650 |
| 4523 |
- >=sci-biology/embassy-iprscan-4.3.1.650 |
| 4524 |
- >=sci-biology/embassy-meme-4.7.650 |
| 4525 |
- >=sci-biology/embassy-mse-3.0.0.650 |
| 4526 |
- >=sci-biology/embassy-phylipnew-3.69.650 |
| 4527 |
- >=sci-biology/embassy-signature-0.1.650 |
| 4528 |
- >=sci-biology/embassy-structure-0.1.650 |
| 4529 |
- >=sci-biology/embassy-topo-2.0.650 |
| 4530 |
- >=sci-biology/embassy-vienna-1.7.2.650" |
| 4531 |
|
| 4532 |
diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml |
| 4533 |
deleted file mode 100644 |
| 4534 |
index f17a827..0000000 |
| 4535 |
--- a/sci-biology/embassy/metadata.xml |
| 4536 |
+++ /dev/null |
| 4537 |
@@ -1,5 +0,0 @@ |
| 4538 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 4539 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 4540 |
-<pkgmetadata> |
| 4541 |
- <herd>sci-biology</herd> |
| 4542 |
-</pkgmetadata> |
| 4543 |
|
| 4544 |
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog |
| 4545 |
deleted file mode 100644 |
| 4546 |
index a6558c1..0000000 |
| 4547 |
--- a/sci-biology/emboss/ChangeLog |
| 4548 |
+++ /dev/null |
| 4549 |
@@ -1,407 +0,0 @@ |
| 4550 |
-# ChangeLog for sci-biology/emboss |
| 4551 |
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
| 4552 |
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ |
| 4553 |
- |
| 4554 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> -emboss-6.3.1_p4-r2.ebuild: |
| 4555 |
- Drop old |
| 4556 |
- |
| 4557 |
- 04 Feb 2015; Justin Lecher <jlec@g.o> metadata.xml: |
| 4558 |
- Clean a bit, user readme.gentoo.eclass |
| 4559 |
- |
| 4560 |
- 04 Jul 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 4561 |
- +files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch, |
| 4562 |
- emboss-6.3.1_p4-r2.ebuild: |
| 4563 |
- sci-biology/emboss-6.3.1_p4-r2: added a patch for 'undefined reference to |
| 4564 |
- c_plwid' bug #493724 |
| 4565 |
- |
| 4566 |
- 24 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 4567 |
- emboss-6.3.1_p4-r2.ebuild: |
| 4568 |
- sci-biology/emboss-6.3.1_p4-r2: add plplot dependency, trying to get rid of a |
| 4569 |
- Makefile.patch using sed hackery |
| 4570 |
- |
| 4571 |
- 16 Sep 2013; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 4572 |
- emboss-6.6.0.ebuild, +files/emboss-6.6.0_plcol.patch: |
| 4573 |
- emboss-6.6.0.ebuild files/emboss-6.6.0_plcol.patch |
| 4574 |
- Added the misisng patch, disabled searches for Gentoo-patches, |
| 4575 |
- fixed patch-related variable values in the 6.6.0 ebuild, BUT |
| 4576 |
- 1) the ebuild does not work, configure exits after looking for |
| 4577 |
- -lhpdf or later -lpng (that can be obeyed by omitting --with-hpdf |
| 4578 |
- --with-pngdriver) |
| 4579 |
- 2) if one relies on whatever configure detects compilation aborts |
| 4580 |
- while compiling embossversion.c or because -lexpat is not in LIBS. |
| 4581 |
- Well, expat is not in configure flags at all. |
| 4582 |
- |
| 4583 |
- Maybe something is caused by the --enable-systemlibs configure switch, |
| 4584 |
- I think it actually enables inclusion of these from their bundled |
| 4585 |
- copies in the EMBOSS tarball (and not use of the system-wide headers |
| 4586 |
- and libs). |
| 4587 |
- |
| 4588 |
-*emboss-6.3.1_p4-r2 (11 Sep 2013) |
| 4589 |
-*emboss-6.5.7 (11 Sep 2013) |
| 4590 |
-*emboss-6.6.0 (11 Sep 2013) |
| 4591 |
- |
| 4592 |
- 11 Sep 2013; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 4593 |
- +emboss-6.3.1_p4-r2.ebuild, +emboss-6.5.7.ebuild, +emboss-6.6.0.ebuild, |
| 4594 |
- +files/ax_lib_mysql.m4, +files/emboss-6.3.1_p4-r2_Makefile.patch, |
| 4595 |
- +files/emboss-6.3.1_p4-r2_compilations-paths.patch, |
| 4596 |
- +files/emboss-6.3.1_p4-r2_libtool.patch, |
| 4597 |
- +files/emboss-6.3.1_p4-r2_plcol.patch, -emboss-6.3.1_p4-r1.ebuild, |
| 4598 |
- -files/emboss-6.3.1_p4-r1_plcol.patch: |
| 4599 |
- Partial success on removal of all crazy libraries and includes from CFLAGS and |
| 4600 |
- LDFLAGS used throught EMBOSS sources. While compile commandline are now clean |
| 4601 |
- still libtool is passed with LDFLAGS carrying over the many X11 and graphics |
| 4602 |
- libraries. Seems the source is ltmain.sh which uses on the linker lines but |
| 4603 |
- editing m4/libtool.m4 is not the right way to do it. Same applies to ltmain.sh |
| 4604 |
- in top-level directory. Any volunteers? Bug #394425 |
| 4605 |
- |
| 4606 |
- 19 Jul 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
| 4607 |
- +files/emboss-6.3.1_p4-r1_plcol.patch, emboss-6.3.1_p4-r1.ebuild: |
| 4608 |
- added plcol patch with increased diff line count, bug #391669; same patch |
| 4609 |
- needs to go into offical emboss-6.3.1_p4 |
| 4610 |
- |
| 4611 |
- 22 May 2012; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild: |
| 4612 |
- Add missing eutils.eclass |
| 4613 |
- |
| 4614 |
- 24 Sep 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild: |
| 4615 |
- Use Fedora hosting because unpstream removed the patches |
| 4616 |
- |
| 4617 |
- 27 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild, |
| 4618 |
- -files/emboss-6.3.1_p4-r1.patch: |
| 4619 |
- Last fix for 64bitness |
| 4620 |
- |
| 4621 |
- 22 Mar 2011; Justin Lecher <jlec@g.o> files/emboss-6.3.1_p4-r1.patch: |
| 4622 |
- Fix compile correctly against postgresql, #359959 |
| 4623 |
- |
| 4624 |
- 21 Mar 2011; Justin Lecher <jlec@g.o> files/emboss-6.3.1_p4-r1.patch: |
| 4625 |
- Implicit decs fix, thanks bicatali for help |
| 4626 |
- |
| 4627 |
- 21 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild, |
| 4628 |
- files/emboss-6.3.1_p4-r1.patch: |
| 4629 |
- Fixed for reviewed eclass |
| 4630 |
- |
| 4631 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild: |
| 4632 |
- Straighten ENV |
| 4633 |
- |
| 4634 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild: |
| 4635 |
- New emboss_src_install used |
| 4636 |
- |
| 4637 |
- 15 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild: |
| 4638 |
- Naming of eclass changed |
| 4639 |
- |
| 4640 |
- 14 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4-r1.ebuild: |
| 4641 |
- Ebov not needed to be set anymore |
| 4642 |
- |
| 4643 |
-*emboss-6.3.1_p4-r1 (11 Mar 2011) |
| 4644 |
- |
| 4645 |
- 11 Mar 2011; Justin Lecher <jlec@g.o> -emboss-6.3.1_p4.ebuild, |
| 4646 |
- +emboss-6.3.1_p4-r1.ebuild, +files/emboss-6.3.1_p4-r1.patch, |
| 4647 |
- -files/emboss-6.3.1_p4.patch: |
| 4648 |
- Rev bump, to ahead of the tree ebuild |
| 4649 |
- |
| 4650 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> -files/6.3.1_p4.patch, |
| 4651 |
- emboss-6.3.1_p4.ebuild, +files/emboss-6.3.1_p4.patch: |
| 4652 |
- Correct naming of patch |
| 4653 |
- |
| 4654 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> metadata.xml: |
| 4655 |
- Removed largefile from local USE description |
| 4656 |
- |
| 4657 |
- 10 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4.ebuild: |
| 4658 |
- Move to new embassy-ng.eclass |
| 4659 |
- |
| 4660 |
- 09 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4.ebuild: |
| 4661 |
- Move to new embassy-ng.eclass |
| 4662 |
- |
| 4663 |
- 09 Mar 2011; Justin Lecher <jlec@g.o> emboss-6.3.1_p4.ebuild: |
| 4664 |
- EAPI=4 takes three arguments on use_with |
| 4665 |
- |
| 4666 |
-*emboss-6.3.1_p4 (09 Mar 2011) |
| 4667 |
- |
| 4668 |
- 09 Mar 2011; Justin Lecher <jlec@g.o> |
| 4669 |
- +files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch, |
| 4670 |
- -emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild: |
| 4671 |
- Bump to latest upstream patches |
| 4672 |
- |
| 4673 |
-*emboss-6.3.1 (09 Mar 2011) |
| 4674 |
- |
| 4675 |
- 09 Mar 2011; Justin Lecher <jlec@g.o> |
| 4676 |
- +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2, |
| 4677 |
- emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild, |
| 4678 |
- +emboss-6.3.1.ebuild, metadata.xml: |
| 4679 |
- Version Bump #335603, Unbundled libs, removed old, fix clash with |
| 4680 |
- /usr/bin/digest, #330507 |
| 4681 |
- |
| 4682 |
- 18 Jul 2010; <nixnut@g.o> emboss-6.0.1.ebuild: |
| 4683 |
- ppc stable #325457 |
| 4684 |
- |
| 4685 |
- 09 Jul 2010; Samuli Suominen <ssuominen@g.o> emboss-6.0.1.ebuild: |
| 4686 |
- ppc64 stable wrt #325457 |
| 4687 |
- |
| 4688 |
- 23 Jun 2010; Justin Lecher <jlec@g.o> emboss-4.0.0.ebuild, |
| 4689 |
- emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild: |
| 4690 |
- Blocking sys-devel/cons, bug 248792 |
| 4691 |
- |
| 4692 |
-*emboss-6.1.0-r1 (07 Mar 2010) |
| 4693 |
- |
| 4694 |
- 07 Mar 2010; Justin Lecher (jlec) <jlec@g.o> |
| 4695 |
- +emboss-6.1.0-r1.ebuild: |
| 4696 |
- Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, |
| 4697 |
- keyworded as in overlay |
| 4698 |
- |
| 4699 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> metadata.xml: |
| 4700 |
- Giving up maintainership of this package. |
| 4701 |
- |
| 4702 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> emboss-6.1.0.ebuild: |
| 4703 |
- Remove documentation that conflicts with EMBASSY phylipnew. |
| 4704 |
- |
| 4705 |
-*emboss-6.1.0 (01 Sep 2009) |
| 4706 |
- |
| 4707 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> +emboss-6.1.0.ebuild: |
| 4708 |
- New upstream version. |
| 4709 |
- |
| 4710 |
- 01 Sep 2009; Olivier Fisette <ribosome@g.o> emboss-6.0.1.ebuild: |
| 4711 |
- Stabilised on x86 and amd64. |
| 4712 |
- |
| 4713 |
- 31 Aug 2009; Olivier Fisette <ribosome@g.o> emboss-4.0.0.ebuild, |
| 4714 |
- emboss-6.0.1.ebuild: |
| 4715 |
- Q.A. fixes, including better dependency on ClustalW. |
| 4716 |
- |
| 4717 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> -emboss-5.0.0.ebuild: |
| 4718 |
- Pruning version that will never be stabilised. |
| 4719 |
- |
| 4720 |
- 27 Aug 2008; Olivier Fisette <ribosome@g.o> emboss-4.0.0.ebuild: |
| 4721 |
- Depend on ClustalW 1.83 since version 2.x will soon be added to Portage |
| 4722 |
- and is incompatible with EMBOSS wrapper programs. |
| 4723 |
- |
| 4724 |
-*emboss-6.0.1 (26 Aug 2008) |
| 4725 |
- |
| 4726 |
- 26 Aug 2008; Olivier Fisette <ribosome@g.o> +emboss-6.0.1.ebuild: |
| 4727 |
- New upstream version. |
| 4728 |
- |
| 4729 |
- 25 Jan 2008; Markus Dittrich <markusle@g.o> |
| 4730 |
- +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild, |
| 4731 |
- emboss-5.0.0.ebuild: |
| 4732 |
- Fixed unresolved symbols with as-needed (see bug #207304). |
| 4733 |
- |
| 4734 |
- 22 Jul 2007; Donnie Berkholz <dberkholz@g.o>; emboss-4.0.0.ebuild: |
| 4735 |
- Drop virtual/x11 references. |
| 4736 |
- |
| 4737 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> |
| 4738 |
- +files/emboss-README.Gentoo-1: |
| 4739 |
- Added updated Gentoo README file in reStructuredText format. |
| 4740 |
- |
| 4741 |
-*emboss-5.0.0 (18 Jul 2007) |
| 4742 |
- |
| 4743 |
- 18 Jul 2007; Olivier Fisette <ribosome@g.o> +emboss-5.0.0.ebuild: |
| 4744 |
- New upstream version. |
| 4745 |
- |
| 4746 |
- 09 Apr 2007; Jeff Gardner <je_fro@g.o> +files/22emboss, |
| 4747 |
- -files/22emboss-r1, emboss-4.0.0.ebuild: |
| 4748 |
- Fixed to use doenvd wrt bug #173884 |
| 4749 |
- |
| 4750 |
- 10 Dec 2006; Olivier Fisette <ribosome@g.o> |
| 4751 |
- -emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild: |
| 4752 |
- Pruned old version. Removed ppc-macos keyword, as grobian said the |
| 4753 |
- package and its dependencies were fully moved into "prefix". |
| 4754 |
- |
| 4755 |
- 20 Nov 2006; <blubb@g.o> emboss-4.0.0.ebuild: |
| 4756 |
- stable on amd64 |
| 4757 |
- |
| 4758 |
- 15 Nov 2006; Markus Rothe <corsair@g.o> emboss-4.0.0.ebuild: |
| 4759 |
- Stable on ppc64; bug #153766 |
| 4760 |
- |
| 4761 |
- 03 Nov 2006; nixnut <nixnut@g.o> emboss-4.0.0.ebuild: |
| 4762 |
- Stable on ppc wrt bug 153766 |
| 4763 |
- |
| 4764 |
- 03 Nov 2006; Jeff Gardner <je_fro@g.o> emboss-3.0.0-r1.ebuild: |
| 4765 |
- Added ~sparc to emboss-3 for embassy-phylip-3.6b. |
| 4766 |
- |
| 4767 |
- 02 Nov 2006; Olivier Fisette <ribosome@g.o> emboss-4.0.0.ebuild: |
| 4768 |
- Added to x86. |
| 4769 |
- |
| 4770 |
- 18 Aug 2006; Jason Wever <weeve@g.o> emboss-4.0.0.ebuild: |
| 4771 |
- Added ~sparc keyword wrt bug #144241. |
| 4772 |
- |
| 4773 |
-*emboss-4.0.0 (21 Jul 2006) |
| 4774 |
- |
| 4775 |
- 21 Jul 2006; Olivier Fisette <ribosome@g.o> +emboss-4.0.0.ebuild: |
| 4776 |
- New upstream version. See change log: |
| 4777 |
- "http://emboss.sourceforge.net/developers/changelog.html". |
| 4778 |
- |
| 4779 |
- 20 Apr 2006; Olivier Fisette <ribosome@g.o> -emboss-3.0.0.ebuild: |
| 4780 |
- Removed old revision. |
| 4781 |
- |
| 4782 |
- 08 Apr 2006; Simon Stelling <blubb@g.o> emboss-3.0.0-r1.ebuild: |
| 4783 |
- stable on amd64 |
| 4784 |
- |
| 4785 |
- 22 Feb 2006; Fabian Groffen <grobian@g.o> ChangeLog: |
| 4786 |
- Marked ppc-macos stable (bug #123332) |
| 4787 |
- |
| 4788 |
- 22 Feb 2006; <nixnut@g.o> emboss-3.0.0-r1.ebuild: |
| 4789 |
- Stable on ppc. bug 123332 |
| 4790 |
- |
| 4791 |
- 21 Feb 2006; Markus Rothe <corsair@g.o> emboss-3.0.0-r1.ebuild: |
| 4792 |
- Stable on ppc64; bug #123332 |
| 4793 |
- |
| 4794 |
- 20 Feb 2006; Joshua Jackson <tsunam@g.o> emboss-3.0.0-r1.ebuild: |
| 4795 |
- Stable on x86; bug #123332 |
| 4796 |
- |
| 4797 |
- 19 Feb 2006; Olivier Fisette <ribosome@g.o> emboss-3.0.0-r1.ebuild: |
| 4798 |
- Block old versions of pscan to avoid file collisions (see bug #116236). |
| 4799 |
- |
| 4800 |
- 23 Jan 2006; Olivier Fisette <ribosome@g.o> +files/README.Gentoo: |
| 4801 |
- Added missing README file (fixes bug #120071). |
| 4802 |
- |
| 4803 |
-*emboss-3.0.0-r1 (21 Jan 2006) |
| 4804 |
- |
| 4805 |
- 21 Jan 2006; Olivier Fisette <ribosome@g.o> |
| 4806 |
- +emboss-3.0.0-r1.ebuild: |
| 4807 |
- Install codons and restriction enzyme equivalence files in alternative |
| 4808 |
- directories. This avoids file collisions on case insensitive filesystems |
| 4809 |
- (see bug #115446), allows the installation of an updated enzyme prototypes |
| 4810 |
- file that will give more consistent results (see bug #118832). |
| 4811 |
- |
| 4812 |
- 14 Dec 2005; Donnie Berkholz <spyderous@g.o>; emboss-3.0.0.ebuild: |
| 4813 |
- Add modular X dependencies. |
| 4814 |
- |
| 4815 |
- 19 Nov 2005; Simon Stelling <blubb@g.o> emboss-3.0.0.ebuild: |
| 4816 |
- stable on amd64 |
| 4817 |
- |
| 4818 |
- 04 Oct 2005; Olivier Fisette <ribosome@g.o> -emboss-2.10.0.ebuild: |
| 4819 |
- Removed obsolete version. |
| 4820 |
- |
| 4821 |
- 03 Oct 2005; Olivier Fisette <ribosome@g.o> emboss-3.0.0.ebuild: |
| 4822 |
- Stable on ppc-macos (with j4rg0n's permission, bug #102420). |
| 4823 |
- |
| 4824 |
- 02 Oct 2005; Michael Hanselmann <hansmi@g.o> emboss-3.0.0.ebuild: |
| 4825 |
- Stable on ppc. |
| 4826 |
- |
| 4827 |
- 24 Sep 2005; Markus Rothe <corsair@g.o> emboss-3.0.0.ebuild: |
| 4828 |
- Stable on ppc64 |
| 4829 |
- |
| 4830 |
- 21 Sep 2005; Olivier Fisette <ribosome@g.o> emboss-3.0.0.ebuild: |
| 4831 |
- Added to x86. |
| 4832 |
- |
| 4833 |
- 04 Sep 2005; Simon Stelling <blubb@g.o> emboss-3.0.0.ebuild: |
| 4834 |
- added ~amd64 keyword |
| 4835 |
- |
| 4836 |
- 13 Aug 2005; Olivier Fisette <ribosome@g.o> emboss-3.0.0.ebuild, |
| 4837 |
- emboss-2.10.0.ebuild: |
| 4838 |
- Fixed Prosite dependency. |
| 4839 |
- |
| 4840 |
-*emboss-3.0.0 (06 Aug 2005) |
| 4841 |
- |
| 4842 |
- 06 Aug 2005; Olivier Fisette <ribosome@g.o> +emboss-3.0.0.ebuild: |
| 4843 |
- New version. |
| 4844 |
- |
| 4845 |
- 28 Jul 2005; Olivier Fisette <ribosome@g.o> -emboss-2.9.0.ebuild: |
| 4846 |
- Removed old version. |
| 4847 |
- |
| 4848 |
- 25 Jun 2005; Lina Pezzella <j4rg0n@g.o> emboss-2.10.0.ebuild: |
| 4849 |
- Stable ppc-macos |
| 4850 |
- |
| 4851 |
- 24 Jun 2005; Joseph Jezak <josejx@g.o> emboss-2.10.0.ebuild: |
| 4852 |
- Marked ppc stable for bug #96819. |
| 4853 |
- |
| 4854 |
- 19 Jun 2005; Markus Rothe <corsair@g.o> emboss-2.10.0.ebuild: |
| 4855 |
- Stable on ppc64 |
| 4856 |
- |
| 4857 |
- 13 May 2005; Olivier Fisette <ribosome@g.o> emboss-2.10.0.ebuild: |
| 4858 |
- Added to x86. |
| 4859 |
- |
| 4860 |
- 02 May 2005; Omkhar Arasaratnam <omkhar@g.o> emboss-2.10.0.ebuild: |
| 4861 |
- Added ~ppc64 |
| 4862 |
- |
| 4863 |
- 02 May 2005; Michael Hanselmann <hansmi@g.o> emboss-2.9.0.ebuild: |
| 4864 |
- Stable on ppc. |
| 4865 |
- |
| 4866 |
-*emboss-2.10.0 (22 Mar 2005) |
| 4867 |
- |
| 4868 |
- 22 Mar 2005; Olivier Fisette <ribosome@g.o> +emboss-2.10.0.ebuild: |
| 4869 |
- New version. |
| 4870 |
- |
| 4871 |
- 22 Feb 2005; Olivier Fisette <ribosome@g.o> emboss-2.9.0.ebuild: |
| 4872 |
- Added support for minimal build. |
| 4873 |
- |
| 4874 |
- 09 Feb 2005; Lina Pezzella <j4rg0n@g.o> emboss-2.9.0.ebuild: |
| 4875 |
- Stable ppc-macos |
| 4876 |
- |
| 4877 |
- 30 Jan 2005; Olivier Fisette <ribosome@g.o> emboss-2.9.0.ebuild: |
| 4878 |
- Ebuild cleanup. |
| 4879 |
- |
| 4880 |
- 01 Jan 2005; Lina Pezzella <j4rg0n@g.o> emboss-2.9.0.ebuild: |
| 4881 |
- Unstable ppc-macos. |
| 4882 |
- |
| 4883 |
-*emboss-2.9.0 (23 Dec 2004) |
| 4884 |
- |
| 4885 |
- 23 Dec 2004; Olivier Fisette <ribosome@g.o> +metadata.xml, |
| 4886 |
- +files/22emboss-r1, +emboss-2.9.0.ebuild: |
| 4887 |
- Moved from app-sci/emboss to sci-biology/emboss. |
| 4888 |
- |
| 4889 |
- 31 Oct 2004; Olivier Fisette <ribosome@g.o> emboss-2.9.0.ebuild, |
| 4890 |
- -emboss-2.8.0-r3.ebuild: |
| 4891 |
- Removed old version. Added 2.9.0 to x86. |
| 4892 |
- |
| 4893 |
- 10 Aug 2004; Olivier Fisette <ribosome@g.o> |
| 4894 |
- emboss-2.8.0-r3.ebuild: |
| 4895 |
- Added to x86. |
| 4896 |
- emboss-2.8.0-r2.ebuild: |
| 4897 |
- Removed obsolete ebuild. |
| 4898 |
- |
| 4899 |
- 21 Jul 2004; David Holm <dholm@g.o> emboss-2.9.0.ebuild: |
| 4900 |
- Added to ~ppc. |
| 4901 |
- |
| 4902 |
- 20 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 4903 |
- emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild: |
| 4904 |
- Removed icc support since no patching is needed. |
| 4905 |
- |
| 4906 |
- 19 Jul 2004; Olivier Fisette <ribosome@g.o> emboss-2.9.0.ebuild: |
| 4907 |
- Version bump. Changed the configuration and install steps a bit to |
| 4908 |
- reflect the fact that header files are now installed automatically. |
| 4909 |
- |
| 4910 |
- 14 Jul 2004; Olivier Fisette <ribosome@g.o> |
| 4911 |
- emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png |
| 4912 |
- USE flags independent; Added support for icc; Added primer3 and clustalw |
| 4913 |
- to the dependencies since some EMBOSS programs won't work without them; |
| 4914 |
- Added support for the biological databases aaindex, cutg, prints, prosite, |
| 4915 |
- rebase and transfac, which are needed for many EMBOSS programs (the databases |
| 4916 |
- are PDEPENDencies since they all must be indexed with an EMBOSS program before |
| 4917 |
- use) (this database support is optional); Added header files installation for |
| 4918 |
- EMBOSS development. |
| 4919 |
- emboss-2.8.0-r2.ebuild: Added to x86. |
| 4920 |
- emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files. |
| 4921 |
- metadata.xml: Added long description; Set myself as maintainer. |
| 4922 |
- |
| 4923 |
- 02 Jun 2004; Aron Griffis <agriffis@g.o> emboss-2.8.0-r1.ebuild, |
| 4924 |
- emboss-2.8.0-r2.ebuild: |
| 4925 |
- Fix use invocation |
| 4926 |
- |
| 4927 |
- 12 May 2004; David Holm <dholm@g.o> emboss-2.8.0-r2.ebuild: |
| 4928 |
- Added to ~ppc. |
| 4929 |
- |
| 4930 |
-*emboss-2.8.0-r2 (11 May 2004) |
| 4931 |
- |
| 4932 |
- 11 May 2004; Patrick Kursawe <phosphan@g.o> emboss-2.8.0-r2.ebuild, |
| 4933 |
- files/22emboss-r1: |
| 4934 |
- Adjusted value of PLPLOT_LIB, see bug #50176 |
| 4935 |
- |
| 4936 |
-*emboss-2.8.0-r1 (30 Jan 2004) |
| 4937 |
- |
| 4938 |
- 30 Jan 2004; Stephen Diener <sediener@g.o> emboss-2.8.0-r1.ebuild: |
| 4939 |
- Modified to use X and png properly for servers |
| 4940 |
- |
| 4941 |
- 28 Jan 2004; Stephen Diener <sediener@g.o> emboss-2.8.0.ebuild: |
| 4942 |
- Modified 2.8.0 ebuild to require X not just USE it. |
| 4943 |
- |
| 4944 |
-*emboss-2.8.0 (13 Dec 2003) |
| 4945 |
- |
| 4946 |
- 13 Dec 2003; Stephen Diener <sediener@g.o> emboss-2.7.1.ebuild, |
| 4947 |
- emboss-2.8.0.ebuild: |
| 4948 |
- Version bump... |
| 4949 |
- |
| 4950 |
- 20 Oct 2003; George Shapovalov <george@g.o> metdata.xml : |
| 4951 |
- added metadata.xml, marked ebuild stable |
| 4952 |
- |
| 4953 |
-*emboss-2.7.1 (03 Sep 2003) |
| 4954 |
- |
| 4955 |
- 03 Sep 2003; <sediener@g.o> emboss-2.7.1.ebuild: |
| 4956 |
- Initial ebuild |
| 4957 |
|
| 4958 |
diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild |
| 4959 |
deleted file mode 100644 |
| 4960 |
index 82f17af..0000000 |
| 4961 |
--- a/sci-biology/emboss/emboss-6.6.0.ebuild |
| 4962 |
+++ /dev/null |
| 4963 |
@@ -1,59 +0,0 @@ |
| 4964 |
-# Copyright 1999-2015 Gentoo Foundation |
| 4965 |
-# Distributed under the terms of the GNU General Public License v2 |
| 4966 |
-# $Header: $ |
| 4967 |
- |
| 4968 |
-EAPI=5 |
| 4969 |
- |
| 4970 |
-AUTOTOOLS_AUTORECONF=1 |
| 4971 |
-inherit autotools-utils emboss-r1 eutils readme.gentoo |
| 4972 |
- |
| 4973 |
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" |
| 4974 |
-SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" |
| 4975 |
- |
| 4976 |
-KEYWORDS="~amd64 ~x86" |
| 4977 |
-IUSE+=" minimal" |
| 4978 |
- |
| 4979 |
-RDEPEND+=" !sys-devel/cons" |
| 4980 |
-PDEPEND+=" |
| 4981 |
- !minimal? ( |
| 4982 |
- sci-biology/aaindex |
| 4983 |
- sci-biology/cutg |
| 4984 |
- sci-biology/prints |
| 4985 |
- sci-biology/prosite |
| 4986 |
- sci-biology/rebase |
| 4987 |
- )" |
| 4988 |
- |
| 4989 |
-S="${WORKDIR}"/EMBOSS-${PV} |
| 4990 |
- |
| 4991 |
-DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ ) |
| 4992 |
- |
| 4993 |
-PATCHES=( |
| 4994 |
- "${FILESDIR}"/${P}_fix-build-system.patch |
| 4995 |
- "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch |
| 4996 |
- "${FILESDIR}"/${P}_plplot-declarations.patch |
| 4997 |
- "${FILESDIR}"/${P}_qa-implicit-declarations.patch |
| 4998 |
-) |
| 4999 |
- |
| 5000 |
-src_install() { |
| 5001 |
- # Use autotools-utils_* to remove useless *.la files |
| 5002 |
- autotools-utils_src_install |
| 5003 |
- |
| 5004 |
- readme.gentoo_create_doc |
| 5005 |
- |
| 5006 |
- # Install env file for setting libplplot and acd files path. |
| 5007 |
- cat > 22emboss <<- EOF |
| 5008 |
- # ACD files location |
| 5009 |
- EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" |
| 5010 |
- EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" |
| 5011 |
- EOF |
| 5012 |
- doenvd 22emboss |
| 5013 |
- |
| 5014 |
- # Remove useless dummy files |
| 5015 |
- find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." |
| 5016 |
- |
| 5017 |
- # Move the provided codon files to a different directory. This will avoid |
| 5018 |
- # user confusion and file collisions on case-insensitive file systems (see |
| 5019 |
- # bug #115446). This change is documented in "README.gentoo". |
| 5020 |
- mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ |
| 5021 |
- die "Failed to move CODON directory." |
| 5022 |
-} |
| 5023 |
|
| 5024 |
diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo |
| 5025 |
deleted file mode 100644 |
| 5026 |
index d1879bd..0000000 |
| 5027 |
--- a/sci-biology/emboss/files/README.gentoo |
| 5028 |
+++ /dev/null |
| 5029 |
@@ -1,34 +0,0 @@ |
| 5030 |
-Administrating EMBOSS on Gentoo systems |
| 5031 |
-======================================= |
| 5032 |
- |
| 5033 |
- |
| 5034 |
-Codon data files location |
| 5035 |
-------------------------- |
| 5036 |
- |
| 5037 |
-The codon data files that are distributed with EMBOSS are installed in the |
| 5038 |
-``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual |
| 5039 |
-``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between |
| 5040 |
-these codon files and those installed with the CUTG database. The names of |
| 5041 |
-these files sometimes vary only by their case. Having both sets of files in |
| 5042 |
-the same directory is also impossible on systems such as MacOSX, where the |
| 5043 |
-root filesystem is case insensitive. If you do not have the CUTG database |
| 5044 |
-installed and want to use the codon files distributed with EMBOSS, you can |
| 5045 |
-symlink the ``CODONS.orig`` directory to ``CODONS``:: |
| 5046 |
- |
| 5047 |
- # cd ${EPREFIX}/usr/share/EMBOSS/data |
| 5048 |
- # ln -s CODONS.orig CODONS |
| 5049 |
- |
| 5050 |
- |
| 5051 |
-Restriction enzymes equivalence file location |
| 5052 |
---------------------------------------------- |
| 5053 |
- |
| 5054 |
-The restriction enzymes equivalence file distributed with EMBOSS is installed |
| 5055 |
-as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual |
| 5056 |
-``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file |
| 5057 |
-collision with the equivalence file provided by the Rebase database. If you do |
| 5058 |
-not have the Rebase database installed and want to use the equivalence file |
| 5059 |
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to |
| 5060 |
-``embossre.equ``:: |
| 5061 |
- |
| 5062 |
- # cd ${EPREFIX}/usr/share/EMBOSS/data |
| 5063 |
- # ln -s embossre.equ.orig embossre.equ |
| 5064 |
|
| 5065 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch |
| 5066 |
deleted file mode 100644 |
| 5067 |
index 7704873..0000000 |
| 5068 |
--- a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch |
| 5069 |
+++ /dev/null |
| 5070 |
@@ -1,11 +0,0 @@ |
| 5071 |
---- EMBOSS-6.6.0/emboss/embossversion.c |
| 5072 |
-+++ EMBOSS-6.6.0/emboss/embossversion.c |
| 5073 |
-@@ -415,7 +415,7 @@ |
| 5074 |
- ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); |
| 5075 |
- #endif |
| 5076 |
- #ifdef _FORTIFY_SOURCE |
| 5077 |
-- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); |
| 5078 |
-+ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); |
| 5079 |
- #endif |
| 5080 |
- ajFmtPrintF(outfile, "\n"); |
| 5081 |
- ajFmtPrintF(outfile, "Sizes (bytes):\n"); |
| 5082 |
|
| 5083 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch |
| 5084 |
deleted file mode 100644 |
| 5085 |
index c831c3b..0000000 |
| 5086 |
--- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch |
| 5087 |
+++ /dev/null |
| 5088 |
@@ -1,368 +0,0 @@ |
| 5089 |
---- EMBOSS-6.6.0/ajax/acd/Makefile.am |
| 5090 |
-+++ EMBOSS-6.6.0/ajax/acd/Makefile.am |
| 5091 |
-@@ -3,16 +3,20 @@ |
| 5092 |
- lib_LTLIBRARIES = libacd.la |
| 5093 |
- |
| 5094 |
- libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
| 5095 |
-+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la |
| 5096 |
- |
| 5097 |
- libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb |
| 5098 |
-+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core |
| 5099 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl |
| 5100 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics |
| 5101 |
--libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5102 |
- if !ESYSTEMLIBS |
| 5103 |
-+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5104 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5105 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
| 5106 |
--endif |
| 5107 |
- libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5108 |
-+else |
| 5109 |
-+libacd_la_CFLAGS += $(PLPLOT_CFLAGS) |
| 5110 |
-+endif |
| 5111 |
- libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
| 5112 |
- |
| 5113 |
- libacd_la_LDFLAGS = -version-info 6:5:0 |
| 5114 |
---- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am |
| 5115 |
-+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am |
| 5116 |
-@@ -3,14 +3,16 @@ |
| 5117 |
- lib_LTLIBRARIES = libajaxdb.la |
| 5118 |
- |
| 5119 |
- libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
| 5120 |
-+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la |
| 5121 |
- |
| 5122 |
- libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl |
| 5123 |
--libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5124 |
-+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core |
| 5125 |
- if !ESYSTEMLIBS |
| 5126 |
-+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5127 |
- libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5128 |
- libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
| 5129 |
--endif |
| 5130 |
- libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5131 |
-+endif |
| 5132 |
- libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) |
| 5133 |
- libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
| 5134 |
- |
| 5135 |
---- EMBOSS-6.6.0/ajax/core/ajreg.h |
| 5136 |
-+++ EMBOSS-6.6.0/ajax/core/ajreg.h |
| 5137 |
-@@ -39,9 +39,8 @@ |
| 5138 |
- #include "ajdefine.h" |
| 5139 |
- #include "ajstr.h" |
| 5140 |
- |
| 5141 |
--#include "pcre_config.h" |
| 5142 |
--#include "pcre_internal.h" |
| 5143 |
--#include "pcreposix.h" |
| 5144 |
-+#include <pcre.h> |
| 5145 |
-+#include <pcreposix.h> |
| 5146 |
- |
| 5147 |
- AJ_BEGIN_DECLS |
| 5148 |
- |
| 5149 |
-@@ -84,7 +83,7 @@ |
| 5150 |
- |
| 5151 |
- typedef struct AjSRegexp |
| 5152 |
- { |
| 5153 |
-- real_pcre *pcre; |
| 5154 |
-+ struct real_pcre *pcre; |
| 5155 |
- pcre_extra *extra; |
| 5156 |
- int *ovector; |
| 5157 |
- const char* orig; |
| 5158 |
---- EMBOSS-6.6.0/ajax/core/Makefile.am |
| 5159 |
-+++ EMBOSS-6.6.0/ajax/core/Makefile.am |
| 5160 |
-@@ -3,13 +3,15 @@ |
| 5161 |
- lib_LTLIBRARIES = libajax.la |
| 5162 |
- |
| 5163 |
- libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
| 5164 |
-+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) |
| 5165 |
- |
| 5166 |
--libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre |
| 5167 |
-+libajax_la_CPPFLAGS = |
| 5168 |
- if !ESYSTEMLIBS |
| 5169 |
-+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5170 |
- libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5171 |
- libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
| 5172 |
--endif |
| 5173 |
- libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5174 |
-+endif |
| 5175 |
- libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
| 5176 |
- libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) |
| 5177 |
- libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) |
| 5178 |
---- EMBOSS-6.6.0/ajax/ensembl/Makefile.am |
| 5179 |
-+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am |
| 5180 |
-@@ -3,13 +3,15 @@ |
| 5181 |
- lib_LTLIBRARIES = libensembl.la |
| 5182 |
- |
| 5183 |
- libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
| 5184 |
-+libensembl_la_LIBADD = ../core/libajax.la |
| 5185 |
- |
| 5186 |
--libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre |
| 5187 |
-+libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core |
| 5188 |
- if !ESYSTEMLIBS |
| 5189 |
-+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5190 |
- libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5191 |
- libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
| 5192 |
--endif |
| 5193 |
- libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5194 |
-+endif |
| 5195 |
- libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
| 5196 |
- |
| 5197 |
- libensembl_la_LDFLAGS = -version-info 6:5:0 |
| 5198 |
---- EMBOSS-6.6.0/ajax/graphics/Makefile.am |
| 5199 |
-+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am |
| 5200 |
-@@ -3,12 +3,16 @@ |
| 5201 |
- lib_LTLIBRARIES = libajaxg.la |
| 5202 |
- |
| 5203 |
- libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
| 5204 |
-+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) |
| 5205 |
- |
| 5206 |
--libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre |
| 5207 |
-+libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core |
| 5208 |
- if !ESYSTEMLIBS |
| 5209 |
-+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5210 |
- libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5211 |
--endif |
| 5212 |
- libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5213 |
-+else |
| 5214 |
-+libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) |
| 5215 |
-+endif |
| 5216 |
- libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) |
| 5217 |
- |
| 5218 |
- libajaxg_la_LDFLAGS = -version-info 6:5:0 |
| 5219 |
---- EMBOSS-6.6.0/ajax/Makefile.am |
| 5220 |
-+++ EMBOSS-6.6.0/ajax/Makefile.am |
| 5221 |
-@@ -1,7 +1,7 @@ |
| 5222 |
- ## Process this file with automake to produce Makefile.in |
| 5223 |
- |
| 5224 |
--SUBDIRS = pcre |
| 5225 |
-+SUBDIRS = |
| 5226 |
- if !ESYSTEMLIBS |
| 5227 |
--SUBDIRS += expat zlib |
| 5228 |
-+SUBDIRS += pcre expat zlib |
| 5229 |
- endif |
| 5230 |
- SUBDIRS += core graphics ensembl ajaxdb acd |
| 5231 |
---- EMBOSS-6.6.0/configure.ac |
| 5232 |
-+++ EMBOSS-6.6.0/configure.ac |
| 5233 |
-@@ -629,32 +629,6 @@ |
| 5234 |
- |
| 5235 |
- |
| 5236 |
- |
| 5237 |
-- |
| 5238 |
--dnl PCRE library definitions - see the MAJOR and MINOR values |
| 5239 |
--dnl to see which version's configure.in these lines come from |
| 5240 |
-- |
| 5241 |
--dnl Provide the current PCRE version information. Do not use numbers |
| 5242 |
--dnl with leading zeros for the minor version, as they end up in a C |
| 5243 |
--dnl macro, and may be treated as octal constants. Stick to single |
| 5244 |
--dnl digits for minor numbers less than 10. There are unlikely to be |
| 5245 |
--dnl that many releases anyway. |
| 5246 |
-- |
| 5247 |
--PCRE_MAJOR="7" |
| 5248 |
--PCRE_MINOR="9" |
| 5249 |
--PCRE_DATE="11-Apr-2009" |
| 5250 |
--PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 5251 |
-- |
| 5252 |
--dnl Default values for miscellaneous macros |
| 5253 |
-- |
| 5254 |
--POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 5255 |
-- |
| 5256 |
--dnl Provide versioning information for libtool shared libraries that |
| 5257 |
--dnl are built by default on Unix systems. |
| 5258 |
-- |
| 5259 |
--PCRE_LIB_VERSION="0:1:0" |
| 5260 |
--PCRE_POSIXLIB_VERSION="0:0:0" |
| 5261 |
-- |
| 5262 |
-- |
| 5263 |
- dnl Define where the EMBOSS package is located |
| 5264 |
- AC_SUBST([AJAX_FIXED_ROOT]) |
| 5265 |
- AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" |
| 5266 |
-@@ -743,17 +717,7 @@ |
| 5267 |
- |
| 5268 |
- |
| 5269 |
- |
| 5270 |
--dnl "Export" these variables for PCRE |
| 5271 |
- |
| 5272 |
--AC_SUBST([HAVE_MEMMOVE]) |
| 5273 |
--AC_SUBST([HAVE_STRERROR]) |
| 5274 |
--AC_SUBST([PCRE_MAJOR]) |
| 5275 |
--AC_SUBST([PCRE_MINOR]) |
| 5276 |
--AC_SUBST([PCRE_DATE]) |
| 5277 |
--AC_SUBST([PCRE_VERSION]) |
| 5278 |
--AC_SUBST([PCRE_LIB_VERSION]) |
| 5279 |
--AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 5280 |
--AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 5281 |
- |
| 5282 |
- |
| 5283 |
- |
| 5284 |
-@@ -849,7 +813,51 @@ |
| 5285 |
- |
| 5286 |
- AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
| 5287 |
- |
| 5288 |
-- |
| 5289 |
-+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
| 5290 |
-+[ |
| 5291 |
-+dnl using system libraries |
| 5292 |
-+ PKG_CHECK_MODULES([PCRE], [libpcre]) |
| 5293 |
-+ PKG_CHECK_MODULES([EXPAT], [expat]) |
| 5294 |
-+ PKG_CHECK_MODULES([ZLIB], [zlib]) |
| 5295 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
| 5296 |
-+], |
| 5297 |
-+[ |
| 5298 |
-+dnl using bundled libraries |
| 5299 |
-+ dnl PCRE library definitions - see the MAJOR and MINOR values |
| 5300 |
-+ dnl to see which version's configure.ac these lines come from |
| 5301 |
-+ |
| 5302 |
-+ dnl Provide the current PCRE version information. Do not use numbers |
| 5303 |
-+ dnl with leading zeros for the minor version, as they end up in a C |
| 5304 |
-+ dnl macro, and may be treated as octal constants. Stick to single |
| 5305 |
-+ dnl digits for minor numbers less than 10. There are unlikely to be |
| 5306 |
-+ dnl that many releases anyway. |
| 5307 |
-+ |
| 5308 |
-+ PCRE_MAJOR="7" |
| 5309 |
-+ PCRE_MINOR="9" |
| 5310 |
-+ PCRE_DATE="11-Apr-2009" |
| 5311 |
-+ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
| 5312 |
-+ |
| 5313 |
-+ dnl Default values for miscellaneous macros |
| 5314 |
-+ |
| 5315 |
-+ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
| 5316 |
-+ |
| 5317 |
-+ dnl Provide versioning information for libtool shared libraries that |
| 5318 |
-+ dnl are built by default on Unix systems. |
| 5319 |
-+ |
| 5320 |
-+ PCRE_LIB_VERSION="0:1:0" |
| 5321 |
-+ PCRE_POSIXLIB_VERSION="0:0:0" |
| 5322 |
-+ |
| 5323 |
-+ dnl "Export" these variables for PCRE |
| 5324 |
-+ AC_SUBST([HAVE_MEMMOVE]) |
| 5325 |
-+ AC_SUBST([HAVE_STRERROR]) |
| 5326 |
-+ AC_SUBST([PCRE_MAJOR]) |
| 5327 |
-+ AC_SUBST([PCRE_MINOR]) |
| 5328 |
-+ AC_SUBST([PCRE_DATE]) |
| 5329 |
-+ AC_SUBST([PCRE_VERSION]) |
| 5330 |
-+ AC_SUBST([PCRE_LIB_VERSION]) |
| 5331 |
-+ AC_SUBST([PCRE_POSIXLIB_VERSION]) |
| 5332 |
-+ AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
| 5333 |
-+]) |
| 5334 |
- |
| 5335 |
- |
| 5336 |
- # Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
| 5337 |
---- EMBOSS-6.6.0/emboss/Makefile.am |
| 5338 |
-+++ EMBOSS-6.6.0/emboss/Makefile.am |
| 5339 |
-@@ -28,15 +28,18 @@ |
| 5340 |
- |
| 5341 |
- AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd |
| 5342 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb |
| 5343 |
-+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core |
| 5344 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl |
| 5345 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics |
| 5346 |
--AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5347 |
- if !ESYSTEMLIBS |
| 5348 |
-+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5349 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5350 |
- AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
| 5351 |
-+AM_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5352 |
-+else |
| 5353 |
-+AM_CFLAGS += $(PLPLOT_CFLAGS) |
| 5354 |
- endif |
| 5355 |
- AM_CPPFLAGS += -I$(top_srcdir)/nucleus |
| 5356 |
--AM_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5357 |
- AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) |
| 5358 |
- AM_CPPFLAGS += $(JAVA_CPPFLAGS) |
| 5359 |
- |
| 5360 |
-@@ -49,9 +52,11 @@ |
| 5361 |
- if !ESYSTEMLIBS |
| 5362 |
- LDADD += ../ajax/zlib/libezlib.la |
| 5363 |
- LDADD += ../ajax/expat/libeexpat.la |
| 5364 |
--endif |
| 5365 |
- LDADD += ../ajax/pcre/libepcre.la |
| 5366 |
- LDADD += ../plplot/libeplplot.la |
| 5367 |
-+else |
| 5368 |
-+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) |
| 5369 |
-+endif |
| 5370 |
- LDADD += $(XLIB) |
| 5371 |
- |
| 5372 |
- #if PURIFY |
| 5373 |
---- EMBOSS-6.6.0/jemboss/lib/Makefile.am |
| 5374 |
-+++ EMBOSS-6.6.0/jemboss/lib/Makefile.am |
| 5375 |
-@@ -12,7 +12,7 @@ |
| 5376 |
- jalviewApplet.jar \ |
| 5377 |
- jemboss.jar |
| 5378 |
- |
| 5379 |
--jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java |
| 5380 |
-+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java |
| 5381 |
- if JAVA_BUILD |
| 5382 |
- $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; |
| 5383 |
- endif |
| 5384 |
---- EMBOSS-6.6.0/m4/idxdbs.m4 |
| 5385 |
-+++ EMBOSS-6.6.0/m4/idxdbs.m4 |
| 5386 |
-@@ -1,17 +1,8 @@ |
| 5387 |
- AC_DEFUN([CHECK_IDXDBS], |
| 5388 |
- [ |
| 5389 |
--AC_MSG_CHECKING(for EMBOSS pre-indexed databases) |
| 5390 |
-+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) |
| 5391 |
- |
| 5392 |
-- |
| 5393 |
--if test -f ./emboss/index/edam.xac; then |
| 5394 |
--AC_MSG_RESULT(yes) |
| 5395 |
--else |
| 5396 |
--AC_MSG_RESULT(no) |
| 5397 |
--echo "" |
| 5398 |
--echo "Pre-indexed edam, taxon + drcat databases not found." |
| 5399 |
--echo "Please download them from within this directory using:" |
| 5400 |
--echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." |
| 5401 |
--echo "and then repeat the configure step." |
| 5402 |
--exit 1 |
| 5403 |
--fi |
| 5404 |
-+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], |
| 5405 |
-+ [], |
| 5406 |
-+ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) |
| 5407 |
- ]) |
| 5408 |
---- EMBOSS-6.6.0/Makefile.am |
| 5409 |
-+++ EMBOSS-6.6.0/Makefile.am |
| 5410 |
-@@ -12,8 +12,11 @@ |
| 5411 |
- ONEWS \ |
| 5412 |
- PROBLEMS |
| 5413 |
- |
| 5414 |
--SUBDIRS = \ |
| 5415 |
--plplot \ |
| 5416 |
-+SUBDIRS = |
| 5417 |
-+if !ESYSTEMLIBS |
| 5418 |
-+SUBDIRS += plplot |
| 5419 |
-+endif |
| 5420 |
-+SUBDIRS += \ |
| 5421 |
- ajax \ |
| 5422 |
- nucleus \ |
| 5423 |
- emboss \ |
| 5424 |
-@@ -33,5 +36,3 @@ |
| 5425 |
- tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) |
| 5426 |
- tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) |
| 5427 |
- |
| 5428 |
--install-exec-hook: |
| 5429 |
-- $(bindir)/embossupdate |
| 5430 |
---- EMBOSS-6.6.0/nucleus/Makefile.am |
| 5431 |
-+++ EMBOSS-6.6.0/nucleus/Makefile.am |
| 5432 |
-@@ -3,6 +3,7 @@ |
| 5433 |
- lib_LTLIBRARIES = libnucleus.la |
| 5434 |
- |
| 5435 |
- libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) |
| 5436 |
-+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la |
| 5437 |
- |
| 5438 |
- if ISSHARED |
| 5439 |
- if ISAIXIA64 |
| 5440 |
-@@ -10,11 +11,14 @@ |
| 5441 |
- endif |
| 5442 |
- endif |
| 5443 |
- |
| 5444 |
--libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot |
| 5445 |
--libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5446 |
-+libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core |
| 5447 |
- if !ESYSTEMLIBS |
| 5448 |
-+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot |
| 5449 |
-+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre |
| 5450 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat |
| 5451 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib |
| 5452 |
-+else |
| 5453 |
-+libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) |
| 5454 |
- endif |
| 5455 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics |
| 5456 |
- libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl |
| 5457 |
|
| 5458 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch |
| 5459 |
deleted file mode 100644 |
| 5460 |
index 15f5f96..0000000 |
| 5461 |
--- a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch |
| 5462 |
+++ /dev/null |
| 5463 |
@@ -1,61 +0,0 @@ |
| 5464 |
---- EMBOSS-6.6.0/ajax/graphics/ajgraph.c |
| 5465 |
-+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c |
| 5466 |
-@@ -49,7 +49,7 @@ |
| 5467 |
- |
| 5468 |
- #define GRAPH_DEBUG 1 |
| 5469 |
- |
| 5470 |
--#include "plplotP.h" |
| 5471 |
-+#include <plplotP.h> |
| 5472 |
- |
| 5473 |
- |
| 5474 |
- static void GraphArray(ajuint numofpoints, |
| 5475 |
-@@ -964,10 +964,10 @@ |
| 5476 |
- if(!thys->ready) |
| 5477 |
- { |
| 5478 |
- #if GRAPH_DEBUG |
| 5479 |
-- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); |
| 5480 |
-+ ajDebug("=g= plsfnam ('%S')\n", txt); |
| 5481 |
- #endif |
| 5482 |
- |
| 5483 |
-- plxsfnam(ajStrGetPtr(txt), ext); |
| 5484 |
-+ plsfnam(ajStrGetPtr(txt)); |
| 5485 |
- ajStrAssignS(&graphBasename, txt); |
| 5486 |
- ajStrAssignC(&graphExtension, ext); |
| 5487 |
- if(ajStrGetCharFirst(graphExtension) == '.') |
| 5488 |
-@@ -1213,10 +1213,10 @@ |
| 5489 |
- void ajGraphicsSetPenwidth(float penwidth) |
| 5490 |
- { |
| 5491 |
- #if GRAPH_DEBUG |
| 5492 |
-- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); |
| 5493 |
-+ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); |
| 5494 |
- #endif |
| 5495 |
- |
| 5496 |
-- plwid((PLINT)penwidth); |
| 5497 |
-+ c_plwidth((PLINT)penwidth); |
| 5498 |
- |
| 5499 |
- return; |
| 5500 |
- } |
| 5501 |
-@@ -1538,10 +1538,10 @@ |
| 5502 |
- static void GraphSetPen(ajint colour) |
| 5503 |
- { |
| 5504 |
- #if GRAPH_DEBUG |
| 5505 |
-- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); |
| 5506 |
-+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); |
| 5507 |
- #endif |
| 5508 |
- |
| 5509 |
-- plcol((PLINT)colour); |
| 5510 |
-+ plcol0((PLINT)colour); |
| 5511 |
- |
| 5512 |
- return; |
| 5513 |
- } |
| 5514 |
---- EMBOSS-6.6.0/ajax/graphics/ajgraph.h |
| 5515 |
-+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h |
| 5516 |
-@@ -32,7 +32,7 @@ |
| 5517 |
- /* ========================================================================= */ |
| 5518 |
- |
| 5519 |
- #include "ajdefine.h" |
| 5520 |
--#include "plplot.h" |
| 5521 |
-+#include <plplot.h> |
| 5522 |
- #include "ajgraphstruct.h" |
| 5523 |
- #include "ajdefine.h" |
| 5524 |
- #include "ajstr.h" |
| 5525 |
|
| 5526 |
diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch |
| 5527 |
deleted file mode 100644 |
| 5528 |
index eff10b2..0000000 |
| 5529 |
--- a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch |
| 5530 |
+++ /dev/null |
| 5531 |
@@ -1,74 +0,0 @@ |
| 5532 |
---- EMBOSS-6.6.0/ajax/core/ajfeatread.c |
| 5533 |
-+++ EMBOSS-6.6.0/ajax/core/ajfeatread.c |
| 5534 |
-@@ -45,6 +45,7 @@ |
| 5535 |
- |
| 5536 |
- #include <limits.h> |
| 5537 |
- #include <math.h> |
| 5538 |
-+#include <string.h> |
| 5539 |
- #include <errno.h> |
| 5540 |
- |
| 5541 |
- #ifdef WIN32 |
| 5542 |
---- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c |
| 5543 |
-+++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c |
| 5544 |
-@@ -43,7 +43,7 @@ |
| 5545 |
- |
| 5546 |
- #include <limits.h> |
| 5547 |
- #include <math.h> |
| 5548 |
-- |
| 5549 |
-+#include <string.h> |
| 5550 |
- |
| 5551 |
- static AjPRegexp featoutRegUfoFmt = NULL; |
| 5552 |
- static AjPRegexp featoutRegUfoFile = NULL; |
| 5553 |
---- EMBOSS-6.6.0/ajax/core/ajpdbio.c |
| 5554 |
-+++ EMBOSS-6.6.0/ajax/core/ajpdbio.c |
| 5555 |
-@@ -37,7 +37,7 @@ |
| 5556 |
- |
| 5557 |
- #include <limits.h> |
| 5558 |
- #include <math.h> |
| 5559 |
-- |
| 5560 |
-+#include <string.h> |
| 5561 |
- |
| 5562 |
- |
| 5563 |
- |
| 5564 |
---- EMBOSS-6.6.0/ajax/core/ajreg.c |
| 5565 |
-+++ EMBOSS-6.6.0/ajax/core/ajreg.c |
| 5566 |
-@@ -32,6 +32,7 @@ |
| 5567 |
- #include "ajlib.h" |
| 5568 |
- |
| 5569 |
- #include "ajreg.h" |
| 5570 |
-+#include <string.h> |
| 5571 |
- |
| 5572 |
- |
| 5573 |
- |
| 5574 |
---- EMBOSS-6.6.0/ajax/core/ajseqtype.c |
| 5575 |
-+++ EMBOSS-6.6.0/ajax/core/ajseqtype.c |
| 5576 |
-@@ -32,7 +32,7 @@ |
| 5577 |
- #include "ajfeat.h" |
| 5578 |
- #include "ajfile.h" |
| 5579 |
- #include "ajreg.h" |
| 5580 |
-- |
| 5581 |
-+#include <string.h> |
| 5582 |
- |
| 5583 |
- |
| 5584 |
- |
| 5585 |
---- EMBOSS-6.6.0/nucleus/embindex.c |
| 5586 |
-+++ EMBOSS-6.6.0/nucleus/embindex.c |
| 5587 |
-@@ -35,6 +35,7 @@ |
| 5588 |
- #include "ajnam.h" |
| 5589 |
- |
| 5590 |
- #include <errno.h> |
| 5591 |
-+#include <string.h> |
| 5592 |
- |
| 5593 |
- #define BTENTRYFILE ".ent" |
| 5594 |
- #define KWLIMIT 12 |
| 5595 |
---- EMBOSS-6.6.0/nucleus/embword.c |
| 5596 |
-+++ EMBOSS-6.6.0/nucleus/embword.c |
| 5597 |
-@@ -36,7 +36,7 @@ |
| 5598 |
- #include "ajutil.h" |
| 5599 |
- |
| 5600 |
- #include <math.h> |
| 5601 |
-- |
| 5602 |
-+#include <string.h> |
| 5603 |
- |
| 5604 |
- |
| 5605 |
- |
| 5606 |
|
| 5607 |
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml |
| 5608 |
deleted file mode 100644 |
| 5609 |
index 3af936d..0000000 |
| 5610 |
--- a/sci-biology/emboss/metadata.xml |
| 5611 |
+++ /dev/null |
| 5612 |
@@ -1,18 +0,0 @@ |
| 5613 |
-<?xml version="1.0" encoding="UTF-8"?> |
| 5614 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 5615 |
-<pkgmetadata> |
| 5616 |
- <herd>sci-biology</herd> |
| 5617 |
- <longdescription> |
| 5618 |
- EMBOSS is "The European Molecular Biology Open Software Suite". |
| 5619 |
- EMBOSS is a free Open Source software analysis package specially |
| 5620 |
- developed for the needs of the molecular biology (e.g. EMBnet) user |
| 5621 |
- community. The software automatically copes with data in a variety |
| 5622 |
- of formats and even allows transparent retrieval of sequence data |
| 5623 |
- from the web. Also, as extensive libraries are provided with the |
| 5624 |
- package, it is a platform to allow other scientists to develop and |
| 5625 |
- release software in true open source spirit. EMBOSS also integrates |
| 5626 |
- a range of currently available packages and tools for sequence |
| 5627 |
- analysis into a seamless whole. EMBOSS breaks the historical trend |
| 5628 |
- towards commercial software packages. |
| 5629 |
- </longdescription> |
| 5630 |
-</pkgmetadata> |
Archives