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From: "Jakov Smolić" <jsmolic@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-libs/rosetta-fragments/, profiles/, sci-libs/rosetta-fragments/files/
Date: Mon, 30 Aug 2021 17:39:28
Message-Id: 1630345127.4ccc9f448c6fef32e56e05502a2ab45a441865c3.jsmolic@gentoo
1 commit: 4ccc9f448c6fef32e56e05502a2ab45a441865c3
2 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
3 AuthorDate: Mon Aug 30 17:14:06 2021 +0000
4 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
5 CommitDate: Mon Aug 30 17:38:47 2021 +0000
6 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4ccc9f44
7
8 sci-libs/rosetta-fragments: Remove last-rited package
9
10 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org>
11
12 profiles/package.mask | 1 -
13 sci-libs/rosetta-fragments/Manifest | 1 -
14 .../files/rosetta-fragments-3.1-chemshift.patch | 62 ---------
15 .../files/rosetta-fragments-3.1-nnmake.patch | 153 ---------------------
16 sci-libs/rosetta-fragments/metadata.xml | 8 --
17 .../rosetta-fragments-3.1-r1.ebuild | 62 ---------
18 6 files changed, 287 deletions(-)
19
20 diff --git a/profiles/package.mask b/profiles/package.mask
21 index 2cb9476c1f4..2d85a7f8cfd 100644
22 --- a/profiles/package.mask
23 +++ b/profiles/package.mask
24 @@ -288,7 +288,6 @@ sci-biology/ncbi-tools
25 sci-biology/njplot
26 sci-biology/psipred
27 sci-chemistry/mars
28 -sci-libs/rosetta-fragments
29
30 # Andreas K. Hüttel <dilfridge@g.o> (2021-07-31)
31 # Obsolete; all versions in current Perl core distributions
32
33 diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest
34 deleted file mode 100644
35 index 838f4129d74..00000000000
36 --- a/sci-libs/rosetta-fragments/Manifest
37 +++ /dev/null
38 @@ -1 +0,0 @@
39 -DIST rosetta3.1_fragments.tgz 221931894 BLAKE2B 0fb5764f24f3386cdbce9afce7da3f81cce91a6a0a57a265e5dbe0bf06146e4ab057c02961ed0dd8074f86309257bcf5b42ca0d1c6adf92c9f8ebf36b3f25f5d SHA512 a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1
40
41 diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
42 deleted file mode 100644
43 index cb8fd9197d1..00000000000
44 --- a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
45 +++ /dev/null
46 @@ -1,62 +0,0 @@
47 - chemshift/make.system | 24 ++++++++++++------------
48 - chemshift/makefile | 2 +-
49 - 2 files changed, 13 insertions(+), 13 deletions(-)
50 -
51 -diff --git a/chemshift/make.system b/chemshift/make.system
52 -index 53bbd38..d105802 100644
53 ---- a/chemshift/make.system
54 -+++ b/chemshift/make.system
55 -@@ -60,18 +60,18 @@ endif
56 - ########## once COMPILER is set, here are the options
57 -
58 - # defaults
59 --F77=f77
60 --FFLAGS=
61 --FOPTIMFLAGS=-O
62 --FDEBUGFLAGS=-g
63 -+F77?=f77
64 -+FFLAGS?=
65 -+FOPTIMFLAGS?=
66 -+FDEBUGFLAGS?=
67 - FPROFILEFLAGS=-P
68 -
69 - ifeq ($(COMPILER),gnu)
70 -- F77 = g77
71 -- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit
72 -- FOPTIMFLAGS = -O -ffast-math -malign-double
73 -- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W
74 -- FPROFILEFLAGS = -pg
75 -+ F77 ?= g77
76 -+ FFLAGS += -W -ffixed-line-length-132 -Wimplicit
77 -+ FOPTIMFLAGS += -malign-double
78 -+ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W
79 -+ FPROFILEFLAGS =
80 - endif
81 -
82 - ifeq ($(COMPILER),pgi) # on mary, good bounds checking
83 -@@ -108,9 +108,9 @@ endif
84 -
85 - # Suse ppc gnu
86 - ifeq ($(COMPILER),ppc)
87 -- F77 = g77
88 -- FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132
89 -- FDEBUGFLAGS = -g -C -Mbounds
90 -+ F77 ?= g77
91 -+ FFLAGS += -Wall -W -ffixed-line-length-132
92 -+ FDEBUGFLAGS += -C -Mbounds
93 - FOPTIMFLAGS =
94 - endif
95 -
96 -diff --git a/chemshift/makefile b/chemshift/makefile
97 -index 712e98f..05d3b64 100644
98 ---- a/chemshift/makefile
99 -+++ b/chemshift/makefile
100 -@@ -64,7 +64,7 @@ regular: compile
101 - # rule to compile executable
102 - compile: $(BASE_NAME).$(COMPILER)
103 - $(BASE_NAME).$(COMPILER) : print ${OBJS}
104 -- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
105 -+ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
106 -
107 - # rule to compile object files:
108 - .$(COMPILER).%.o: %.f
109
110 diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch
111 deleted file mode 100644
112 index 91da48017ef..00000000000
113 --- a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch
114 +++ /dev/null
115 @@ -1,153 +0,0 @@
116 - nnmake/dipolar_nn.f | 2 +-
117 - nnmake/make.system | 33 ++++++++++++++++-----------------
118 - nnmake/make_fragments.pl | 36 ++++++++++++++++++------------------
119 - nnmake/makefile | 2 +-
120 - 4 files changed, 36 insertions(+), 37 deletions(-)
121 -
122 -diff --git a/nnmake/dipolar_nn.f b/nnmake/dipolar_nn.f
123 -index c159888..4412a20 100644
124 ---- a/nnmake/dipolar_nn.f
125 -+++ b/nnmake/dipolar_nn.f
126 -@@ -1396,7 +1396,7 @@ car pairDipolar(1,i) .le. pairDipolar(1,i+1)
127 - write(0,*)'rejected'
128 - write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset)
129 - do i=1,maplength(iset)
130 -- write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5),
131 -+ write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5),
132 - # b(i)
133 - enddo
134 - goto 300
135 -diff --git a/nnmake/make.system b/nnmake/make.system
136 -index 34bea8f..2fbfabf 100644
137 ---- a/nnmake/make.system
138 -+++ b/nnmake/make.system
139 -@@ -55,18 +55,17 @@ endif
140 - ########## once COMPILER is set, here are the options
141 -
142 - # defaults
143 --F77=f77
144 --FFLAGS=
145 --FOPTIMFLAGS=-O
146 --FDEBUGFLAGS=-g
147 --FPROFILEFLAGS=-P
148 -+F77?=f77
149 -+FOPTIMFLAGS=
150 -+FDEBUGFLAGS=
151 -+FPROFILEFLAGS=
152 -
153 - ifeq ($(COMPILER),gnu)
154 -- F77 = g77
155 -- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit
156 -- FOPTIMFLAGS = -O -ffast-math -malign-double
157 -- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W
158 -- FPROFILEFLAGS = -pg
159 -+ F77 ?= g77
160 -+ FFLAGS += -W -ffixed-line-length-132 -Wimplicit
161 -+ FOPTIMFLAGS += -malign-double
162 -+ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W
163 -+ FPROFILEFLAGS =
164 - endif
165 -
166 - ifeq ($(COMPILER),pgi) # on mary, good bounds checking
167 -@@ -82,9 +81,9 @@ ifeq ($(COMPILER),pgi) # on mary, good bounds checking
168 - endif
169 -
170 - ifeq ($(COMPILER),absoft) # on mary, fast
171 -- F77 = f77
172 -- FFLAGS = -N109 -s -W
173 -- LINKFLAGS = -lU77
174 -+ F77 ?= f77
175 -+ FFLAGS ?= -N109 -s -W
176 -+ LINKFLAGS += -lU77
177 - FDEBUGFLAGS = -C -g
178 - FOPTIMFLAGS = -O -N18
179 - FPROFILEFLAGS = -P -O
180 -@@ -103,10 +102,10 @@ endif
181 -
182 - # Suse ppc gnu
183 - ifeq ($(COMPILER),ppc)
184 -- F77 = g77
185 -- FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132
186 -- FDEBUGFLAGS = -g -C -Mbounds
187 -- FOPTIMFLAGS =
188 -+ F77 ?= g77
189 -+ FFLAGS += -Wall -W -ffixed-line-length-132
190 -+ FDEBUGFLAGS += -C -Mbounds
191 -+ FOPTIMFLAGS +=
192 - endif
193 -
194 - # alpha flags
195 -diff --git a/nnmake/make_fragments.pl b/nnmake/make_fragments.pl
196 -index 5273685..29619a2 100755
197 ---- a/nnmake/make_fragments.pl
198 -+++ b/nnmake/make_fragments.pl
199 -@@ -19,38 +19,38 @@
200 -
201 - my $TAIL = "_v1_3";
202 -
203 --$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments';
204 --$shareware_dir = '/work/chu/src/shareware';
205 --$scratch = "/scratch/shared";
206 -+$src_dir = '@GENTOO_PORTAGE_EPREFIX@/';
207 -+$shareware_dir = '$src_dir/usr/share';
208 -+$scratch = "$src_dir/scratch/shared";
209 -
210 - # psi-blast
211 - #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin";
212 --my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp"; # PSI-BLAST (duh.)
213 --my $NR = "/$scratch/genomes/nr"; # nr blast database filename
214 --my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database')
215 --my $BLOSUM = "$scratch/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database')
216 -+my $PSIBLAST = "$src_dir/usr/bin/blastpgp"; # PSI-BLAST (duh.)
217 -+my $NR = "$shareware_dir/nr"; # nr blast database filename
218 -+my $VALL_BLAST_DB = "$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database')
219 -+my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database')
220 -
221 - # psipred
222 --my $FILTNR = "$scratch/genomes/filtnr"; # filtnr blast database filename
223 --my $MAKEMAT = "$shareware_dir/blast/bin/makemat"; # makemat utility (part of NCBI tools)
224 --my $PSIPRED = "$shareware_dir/psipred/bin/psipred"; # psipred
225 --my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2"; # psipass2 (part of psipred pkg)
226 -+my $FILTNR = "$src_dir/tmp/filtnr"; # filtnr blast database filename
227 -+my $MAKEMAT = "$src_dir/usr/bin/makemat"; # makemat utility (part of NCBI tools)
228 -+my $PSIPRED = "$src_dir/usr/bin/psipred"; # psipred
229 -+my $PSIPASS2 = "$src_dir/usr/bin/psipass2"; # psipass2 (part of psipred pkg)
230 - my $PSIPRED_DATA = "$shareware_dir/psipred/data"; # dir containing psipred data files.
231 -
232 - # prof
233 - #my $PROF = "$shareware_dir/prof/run_prof.py";
234 --my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof executable location in run_prof.py
235 -+my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof executable location in run_prof.py
236 -
237 - # nnmake
238 --my $VALL = "$scratch/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database')
239 --my $VALL2 = "$scratch/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database')
240 -+my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database')
241 -+my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database')
242 - my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist)
243 --my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu"; # nnmake binary (cvs respository 'nnmake')
244 --my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake')
245 -+my $NNMAKE = "$src_dir/usr/bin/pNNMAKE"; # nnmake binary (cvs respository 'nnmake')
246 -+my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake')
247 -
248 - # chemshift
249 --my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary (cvs repository 'chemshift')
250 --my $TALOS_DB = "$scratch/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database')
251 -+my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT"; # chemshift binary (cvs repository 'chemshift')
252 -+my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database')
253 -
254 - # jufo (secondary structure prediction software)
255 - my $JUFO = "$shareware_dir/jufo/molecule.exe"; # jufo executable
256 -diff --git a/nnmake/makefile b/nnmake/makefile
257 -index c09ac1c..ebfde68 100644
258 ---- a/nnmake/makefile
259 -+++ b/nnmake/makefile
260 -@@ -102,7 +102,7 @@ VallCoord: coord_compile
261 - # rule to compile executable
262 - compile: print $(BASE_NAME).$(COMPILER)
263 - $(BASE_NAME).$(COMPILER) : ${OBJS}
264 -- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
265 -+ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
266 -
267 - coord_compile: print $(COORD_BASE_NAME).$(COMPILER)
268 - $(COORD_BASE_NAME).$(COMPILER) : ${COORD_OBJS}
269
270 diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml
271 deleted file mode 100644
272 index 8937bad0b17..00000000000
273 --- a/sci-libs/rosetta-fragments/metadata.xml
274 +++ /dev/null
275 @@ -1,8 +0,0 @@
276 -<?xml version="1.0" encoding="UTF-8"?>
277 -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
278 -<pkgmetadata>
279 - <maintainer type="project">
280 - <email>sci-chemistry@g.o</email>
281 - <name>Gentoo Chemistry Project</name>
282 - </maintainer>
283 -</pkgmetadata>
284
285 diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
286 deleted file mode 100644
287 index bc262a212a4..00000000000
288 --- a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
289 +++ /dev/null
290 @@ -1,62 +0,0 @@
291 -# Copyright 1999-2021 Gentoo Authors
292 -# Distributed under the terms of the GNU General Public License v2
293 -
294 -EAPI=6
295 -
296 -inherit flag-o-matic prefix toolchain-funcs vcs-clean
297 -
298 -DESCRIPTION="Fragment library for rosetta"
299 -HOMEPAGE="http://www.rosettacommons.org"
300 -SRC_URI="rosetta3.1_fragments.tgz"
301 -
302 -LICENSE="rosetta"
303 -SLOT="0"
304 -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
305 -IUSE=""
306 -
307 -DEPEND=""
308 -RDEPEND="
309 - sci-biology/ncbi-tools
310 - sci-biology/update-blastdb
311 - sci-biology/psipred"
312 -
313 -RESTRICT="fetch"
314 -
315 -S="${WORKDIR}"/${PN/-/_}
316 -
317 -PATCHES=(
318 - "${FILESDIR}"/${P}-nnmake.patch
319 - "${FILESDIR}"/${P}-chemshift.patch
320 -)
321 -
322 -pkg_nofetch() {
323 - einfo "Go to ${HOMEPAGE} and get ${PN}.tgz and rename it to ${A}"
324 - einfo "which must be placed into your DISTDIR directory."
325 -}
326 -
327 -src_prepare() {
328 - default
329 - tc-export F77
330 - eprefixify nnmake/*.pl
331 -}
332 -
333 -src_compile() {
334 - emake -C nnmake
335 - emake -C chemshift
336 -}
337 -
338 -src_install() {
339 - esvn_clean .
340 -
341 - newbin nnmake/pNNMAKE.gnu pNNMAKE
342 - newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT
343 -
344 - dobin nnmake/*.pl
345 -
346 - insinto /usr/share/${PN}
347 - doins -r *_database
348 - dodoc \
349 - fragments.README \
350 - nnmake/{nnmake.README,vall/*.pl} \
351 - chemshift/chemshift.README
352 -}
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