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commit: 2e1af23d4b6f4751d84eb7ab519b090db71c83d7 |
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Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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AuthorDate: Sat Dec 9 23:27:11 2017 +0000 |
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Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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CommitDate: Sun Dec 10 00:05:30 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2e1af23d |
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|
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sci-biology/wise: Move patches to a distfile |
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|
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Closes: https://bugs.gentoo.org/620622 |
11 |
|
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sci-biology/wise/Manifest | 3 +- |
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.../wise/files/wise-2.4.0_alpha-cflags.patch | 407 --------------------- |
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.../wise/files/wise-2.4.0_alpha-glibc-2.10.patch | 302 --------------- |
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sci-biology/wise/files/wise-api.tex.patch | 38 -- |
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sci-biology/wise/files/wise-env | 1 - |
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sci-biology/wise/wise-2.4.0_alpha.ebuild | 11 +- |
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6 files changed, 8 insertions(+), 754 deletions(-) |
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|
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diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest |
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index fc9cf9f0083..f9c6fa852c5 100644 |
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--- a/sci-biology/wise/Manifest |
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+++ b/sci-biology/wise/Manifest |
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@@ -1 +1,2 @@ |
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-DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec |
26 |
+DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe |
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+DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c |
28 |
|
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diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch |
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deleted file mode 100644 |
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index d3c17098105..00000000000 |
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--- a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch |
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+++ /dev/null |
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@@ -1,407 +0,0 @@ |
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-diff --git a/src/base/makefile b/src/base/makefile |
36 |
-index 4620f19..a84e2c7 100644 |
37 |
---- a/src/base/makefile |
38 |
-+++ b/src/base/makefile |
39 |
-@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \ |
40 |
- |
41 |
- |
42 |
- #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH |
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--CFLAGS = -c -O2 -DUNIX -pthread |
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--LFLAGS = -g -lm |
45 |
-+CFLAGS += -c -DUNIX -pthread |
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-+LFLAGS = -lm |
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- DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D |
48 |
- AR_OPTIONS = ru |
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- |
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-diff --git a/src/corba/makefile b/src/corba/makefile |
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-index df3dd78..237a1ba 100644 |
52 |
---- a/src/corba/makefile |
53 |
-+++ b/src/corba/makefile |
54 |
-@@ -1,10 +1,10 @@ |
55 |
- |
56 |
- |
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--CC = cc |
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-+CC += gcc |
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- INCFLAGS = -I../base/ -I../dynlibsrc |
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- #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ |
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--#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ |
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--CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` |
63 |
-+#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/ |
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-+CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags` |
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- LFLAGS = -L../base/ -lm -lpthread |
66 |
- AR_OPTIONS = ru |
67 |
- |
68 |
-@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl |
69 |
- orbit-idl hspscan_corba.idl |
70 |
- |
71 |
- test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o |
72 |
-- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
73 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
74 |
- |
75 |
- scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o |
76 |
-- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
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-+ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
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- |
79 |
- |
80 |
- test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o |
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-- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
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-+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
83 |
- |
84 |
- |
85 |
- test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o |
86 |
-- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
87 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread |
88 |
- |
89 |
- .c.o : |
90 |
- $(CC) $(CFLAGS) $(INCFLAGS) $? |
91 |
-diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile |
92 |
-index ef3334a..3a0bc2a 100644 |
93 |
---- a/src/dnaindex/assembly/makefile |
94 |
-+++ b/src/dnaindex/assembly/makefile |
95 |
-@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o |
96 |
- |
97 |
- |
98 |
- CC = cc |
99 |
--CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` |
100 |
-+CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags` |
101 |
- |
102 |
- |
103 |
--LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm |
104 |
-+LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm |
105 |
- |
106 |
- |
107 |
- .c.o : |
108 |
-diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile |
109 |
-index 285e6a0..8c6a0dc 100644 |
110 |
---- a/src/dnaindex/makefile |
111 |
-+++ b/src/dnaindex/makefile |
112 |
-@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) |
113 |
- |
114 |
- |
115 |
- kwise : kwise.o $(ASSEMBLY_OBJ) |
116 |
-- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` |
117 |
-+ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` |
118 |
- |
119 |
- arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) |
120 |
-- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` |
121 |
-+ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` |
122 |
- |
123 |
- |
124 |
- findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) |
125 |
-- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` |
126 |
-+ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` |
127 |
- |
128 |
- make_shotgun : make_shotgun.o shotgun.o |
129 |
- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) |
130 |
-@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o |
131 |
- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) |
132 |
- |
133 |
- CC = cc |
134 |
--CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` |
135 |
-+CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` |
136 |
- |
137 |
- |
138 |
--LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm |
139 |
-+LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm |
140 |
- |
141 |
- |
142 |
- .c.o : |
143 |
-diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile |
144 |
-index d1d77af..cad8900 100644 |
145 |
---- a/src/dynlibsrc/makefile |
146 |
-+++ b/src/dynlibsrc/makefile |
147 |
-@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \ |
148 |
- |
149 |
- |
150 |
- |
151 |
--CC = cc |
152 |
-+CC ?= gcc |
153 |
- INCFLAGS = -I../base/ |
154 |
- #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ |
155 |
--CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` |
156 |
--#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` |
157 |
-+CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` |
158 |
-+#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` |
159 |
- #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ |
160 |
- LFLAGS = -g -L../base/ -lm |
161 |
- AR_OPTIONS = ru |
162 |
-@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a |
163 |
- $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm |
164 |
- |
165 |
- test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a |
166 |
-- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm |
167 |
-+ $(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm |
168 |
- |
169 |
- test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o |
170 |
-- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` |
171 |
-+ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` |
172 |
- |
173 |
- test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o |
174 |
-- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` |
175 |
-+ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` |
176 |
- |
177 |
- |
178 |
- testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o |
179 |
-diff --git a/src/external/mott/makefile b/src/external/mott/makefile |
180 |
-index 8d7c1d4..940c438 100644 |
181 |
---- a/src/external/mott/makefile |
182 |
-+++ b/src/external/mott/makefile |
183 |
-@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o |
184 |
- wise2_mott_bridge.o : wise2_mott_bridge.c |
185 |
- $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c |
186 |
- |
187 |
--CC = cc |
188 |
-+CC ?= gcc |
189 |
- |
190 |
--CFLAGS = -Wall -g3 -DPTHREAD -O2 -c |
191 |
--LFLAGS = -g -L../base/ -lm |
192 |
-+CFLAGS += -DPTHREAD -c |
193 |
-+LFLAGS = -L../base/ -lm |
194 |
- AR_OPTIONS = ru |
195 |
- |
196 |
- |
197 |
-diff --git a/src/makefile b/src/makefile |
198 |
-index bdff4ff..0d7c871 100644 |
199 |
---- a/src/makefile |
200 |
-+++ b/src/makefile |
201 |
-@@ -26,12 +26,12 @@ |
202 |
- |
203 |
- # Change the cc line to gcc if you get compiler errors |
204 |
- # Most likely you have a non ANSI C compiler |
205 |
--CC ?= cc |
206 |
-+CC ?= gcc |
207 |
- |
208 |
- # These are the CFLAGS to use. These days Wise2 is inherently |
209 |
- # pthreaded, and everything is compiled with threads. More |
210 |
- # info on running threads can be found in the documentation |
211 |
--CFLAGS = -c -pthread -O2 `glib-config --cflags` |
212 |
-+CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags` |
213 |
- |
214 |
- |
215 |
- |
216 |
-diff --git a/src/models/makefile b/src/models/makefile |
217 |
-index f518d0c..a297eff 100644 |
218 |
---- a/src/models/makefile |
219 |
-+++ b/src/models/makefile |
220 |
-@@ -50,6 +50,8 @@ NEWG = geneparser21.o \ |
221 |
- proteinsw.o \ |
222 |
- estquick3.o |
223 |
- |
224 |
-+EXTRALIBS += `pkg-config glib-2.0 --libs` |
225 |
-+ |
226 |
- all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a |
227 |
- |
228 |
- libmodel.a : $(NEWG) |
229 |
-@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c |
230 |
- $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. |
231 |
- |
232 |
- oldpostwise : oldpostwise.o $(NEWG) |
233 |
-- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm |
234 |
-+ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm |
235 |
- |
236 |
- testdna : testdna.o dnaalign.o seqaligndisplay.o |
237 |
- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
238 |
-@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o |
239 |
- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
240 |
- |
241 |
- scanwisep.o : scanwisep.c |
242 |
-- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? |
243 |
-+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $? |
244 |
- |
245 |
- hsp2aln_sw.o : hsp2aln_sw.c |
246 |
-- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? |
247 |
-+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? |
248 |
- |
249 |
- scanwisep_mysql.o : scanwisep.c |
250 |
- $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c |
251 |
-@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc. |
252 |
- |
253 |
- |
254 |
- scanwisep_wiseserver.o : scanwisep.c |
255 |
-- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c |
256 |
-+ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` |
257 |
- |
258 |
- scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o |
259 |
-- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread |
260 |
-+ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs` |
261 |
- |
262 |
- scanwisep_compress.o : scanwisep.c |
263 |
- $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c |
264 |
-@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap. |
265 |
- |
266 |
- |
267 |
- scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o |
268 |
-- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread |
269 |
-+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread |
270 |
- |
271 |
- test_gwhsp : test_gwhsp.o genewisehsp.o |
272 |
-- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread |
273 |
-+ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread |
274 |
- |
275 |
- localcishit.o : localcishit.c |
276 |
-- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? |
277 |
-+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? |
278 |
- |
279 |
- promoterwise.o : promoterwise.c |
280 |
-- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? |
281 |
-+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? |
282 |
- |
283 |
- promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o |
284 |
-- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread |
285 |
-+ $(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread |
286 |
- |
287 |
- test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o |
288 |
-- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread |
289 |
-+ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread |
290 |
- |
291 |
- promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o |
292 |
-- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread |
293 |
-+ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread |
294 |
- |
295 |
- dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o |
296 |
- $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread |
297 |
-@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o |
298 |
- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
299 |
- |
300 |
- genewise : genewise.o $(NEWG) |
301 |
-- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
302 |
-+ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` |
303 |
- |
304 |
- cdnawise : cdnawise.o $(NEWG) cdnawise10.o |
305 |
-- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
306 |
-+ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
307 |
- |
308 |
- fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o |
309 |
-- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
310 |
-+ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
311 |
- |
312 |
- |
313 |
- fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o |
314 |
-- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
315 |
-+ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
316 |
- |
317 |
- fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o |
318 |
-- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
319 |
-+ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
320 |
- |
321 |
- |
322 |
- editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o |
323 |
-- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm |
324 |
-+ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm |
325 |
- |
326 |
- |
327 |
- efgw : genewise.o $(NEWG) |
328 |
-- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence |
329 |
-+ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence |
330 |
- |
331 |
- |
332 |
- genewisedb : genewisedb.o $(NEWG) |
333 |
-- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
334 |
-+ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` |
335 |
- |
336 |
- estwisedb : estwisedb.o $(NEWG) |
337 |
-- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
338 |
-+ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` |
339 |
- |
340 |
- edb : estwisedb.o $(NEWG) |
341 |
-- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence |
342 |
-+ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence |
343 |
- |
344 |
- estwise : estwise.o $(NEWG) |
345 |
-- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
346 |
-+ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` |
347 |
- |
348 |
- |
349 |
- amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o |
350 |
-- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
351 |
-+ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
352 |
- |
353 |
- genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o |
354 |
-- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
355 |
-+ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
356 |
- |
357 |
- sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o |
358 |
-- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
359 |
-+ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
360 |
- |
361 |
- alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o |
362 |
-- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
363 |
-+ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
364 |
- |
365 |
- test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o |
366 |
-- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
367 |
-+ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
368 |
- |
369 |
- statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o |
370 |
-- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
371 |
-+ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
372 |
- |
373 |
- pseudowise : pseudowise.o pseudowise7.o $(NEWG) |
374 |
-- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
375 |
-+ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` |
376 |
- |
377 |
- clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o |
378 |
-- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
379 |
-+ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) |
380 |
- |
381 |
- |
382 |
- HMMER_LIBS = ../HMMer2/ |
383 |
-@@ -345,11 +347,11 @@ HMMER_DEFINE = |
384 |
- CC = cc |
385 |
- #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ |
386 |
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. |
387 |
--CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` |
388 |
--#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` |
389 |
-+CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` |
390 |
-+#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` |
391 |
- #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ |
392 |
- |
393 |
--LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` |
394 |
-+LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs` |
395 |
- AR_OPTIONS = ru |
396 |
- |
397 |
- RANLIB_NEEDED = 0 |
398 |
-diff --git a/src/network/makefile b/src/network/makefile |
399 |
-index 303c2da..e607310 100644 |
400 |
---- a/src/network/makefile |
401 |
-+++ b/src/network/makefile |
402 |
-@@ -3,8 +3,8 @@ |
403 |
- |
404 |
- CC = cc |
405 |
- INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex |
406 |
--CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` |
407 |
--LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` |
408 |
-+CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags` |
409 |
-+LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` |
410 |
- AR_OPTIONS = ru |
411 |
- |
412 |
- RANLIB_NEEDED = 0 |
413 |
-diff --git a/src/snp/makefile b/src/snp/makefile |
414 |
-index ccf750a..2b83c43 100644 |
415 |
---- a/src/snp/makefile |
416 |
-+++ b/src/snp/makefile |
417 |
-@@ -2,12 +2,12 @@ |
418 |
- .SUFFIXES : .dy |
419 |
- |
420 |
- |
421 |
--CC = cc |
422 |
-+CC ?= gcc |
423 |
- #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ |
424 |
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. |
425 |
--CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` |
426 |
-+CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` |
427 |
- |
428 |
--LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm |
429 |
-+LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm |
430 |
- AR_OPTIONS = ru |
431 |
- |
432 |
- RANLIB_NEEDED = 0 |
433 |
-@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0 |
434 |
- $(CC) $(CFLAGS) $(INCFLAGS) $? |
435 |
- |
436 |
- test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o |
437 |
-- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) |
438 |
-+ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) |
439 |
- |
440 |
- INCFLAGS = -I../base/ -I../dynlibsrc/ |
441 |
- DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn |
442 |
|
443 |
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch |
444 |
deleted file mode 100644 |
445 |
index 42af0c7e849..00000000000 |
446 |
--- a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch |
447 |
+++ /dev/null |
448 |
@@ -1,302 +0,0 @@ |
449 |
-diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c |
450 |
-index 5889e7d..bc95629 100644 |
451 |
---- a/src/HMMer2/sqio.c |
452 |
-+++ b/src/HMMer2/sqio.c |
453 |
-@@ -213,7 +213,7 @@ readline(FILE *f, char *s) |
454 |
- } |
455 |
- } |
456 |
- |
457 |
--/* Function: getline() |
458 |
-+/* Function: get_line() |
459 |
- * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] |
460 |
- * |
461 |
- * Purpose: read a line from a sequence file into V->sbuffer. |
462 |
-@@ -229,7 +229,7 @@ readline(FILE *f, char *s) |
463 |
- * Returns: (void) |
464 |
- */ |
465 |
- static void |
466 |
--getline(struct ReadSeqVars *V) |
467 |
-+get_line(struct ReadSeqVars *V) |
468 |
- { |
469 |
- char *cp; |
470 |
- |
471 |
-@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) |
472 |
- V->seqlen = 0; |
473 |
- if (addfirst) addseq(V->sbuffer, V); |
474 |
- do { |
475 |
-- getline(V); |
476 |
-+ get_line(V); |
477 |
- /* feof() alone is a bug; files not necessarily \n terminated */ |
478 |
- if (*(V->sbuffer) == '\0' && feof(V->f)) |
479 |
- done = TRUE; |
480 |
-@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V) |
481 |
- char *sptr; |
482 |
- /* load first line of entry */ |
483 |
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) |
484 |
-- getline(V); |
485 |
-+ get_line(V); |
486 |
- if (feof(V->f)) return; |
487 |
- |
488 |
- if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) |
489 |
-@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V) |
490 |
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); |
491 |
- } |
492 |
- do { |
493 |
-- getline(V); |
494 |
-+ get_line(V); |
495 |
- if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) |
496 |
- SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); |
497 |
- else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) |
498 |
-@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V) |
499 |
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); |
500 |
- } |
501 |
- } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); |
502 |
-- getline(V); /* skip next line, coords */ |
503 |
-+ get_line(V); /* skip next line, coords */ |
504 |
- |
505 |
- readLoop(0, endPIR, V); |
506 |
- |
507 |
-@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V) |
508 |
- /* get next line |
509 |
- */ |
510 |
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) |
511 |
-- getline(V); |
512 |
-+ get_line(V); |
513 |
- } |
514 |
- |
515 |
- |
516 |
-@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V) |
517 |
- char *nm; |
518 |
- /* position past ';' comments */ |
519 |
- do { |
520 |
-- getline(V); |
521 |
-+ get_line(V); |
522 |
- } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); |
523 |
- |
524 |
- if (!feof(V->f)) |
525 |
-@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V) |
526 |
- } |
527 |
- |
528 |
- while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) |
529 |
-- getline(V); |
530 |
-+ get_line(V); |
531 |
- } |
532 |
- |
533 |
- static int |
534 |
-@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V) |
535 |
- if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) |
536 |
- SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); |
537 |
- } |
538 |
-- getline(V); |
539 |
-+ get_line(V); |
540 |
- } |
541 |
- |
542 |
- if (! feof(V->f)) |
543 |
-@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V) |
544 |
- /* load next line |
545 |
- */ |
546 |
- while ((!feof(V->f)) && (*V->sbuffer != ';')) |
547 |
-- getline(V); |
548 |
-+ get_line(V); |
549 |
- } |
550 |
- |
551 |
- |
552 |
-@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V) |
553 |
- int in_definition; |
554 |
- |
555 |
- while (strncmp(V->sbuffer, "LOCUS", 5) != 0) |
556 |
-- getline(V); |
557 |
-+ get_line(V); |
558 |
- |
559 |
- if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) |
560 |
- { |
561 |
-@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V) |
562 |
- in_definition = FALSE; |
563 |
- while (! feof(V->f)) |
564 |
- { |
565 |
-- getline(V); |
566 |
-+ get_line(V); |
567 |
- if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) |
568 |
- { |
569 |
- if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) |
570 |
-@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V) |
571 |
- |
572 |
- |
573 |
- while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) |
574 |
-- getline(V); |
575 |
-+ get_line(V); |
576 |
- /* SRE: V->s now holds "//", so sequential |
577 |
- reads are wedged: fixed Tue Jul 13 1993 */ |
578 |
- while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) |
579 |
-- getline(V); |
580 |
-+ get_line(V); |
581 |
- } |
582 |
- |
583 |
- static int |
584 |
-@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V) |
585 |
- Die("bogus GCGdata format? %s", V->sbuffer); |
586 |
- |
587 |
- /* second line contains free text description */ |
588 |
-- getline(V); |
589 |
-+ get_line(V); |
590 |
- SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); |
591 |
- |
592 |
- if (binary) { |
593 |
-@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V) |
594 |
- else readLoop(0, endGCGdata, V); |
595 |
- |
596 |
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) |
597 |
-- getline(V); |
598 |
-+ get_line(V); |
599 |
- } |
600 |
- |
601 |
- static int |
602 |
-@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V) |
603 |
- if ((sptr = strtok(NULL, "\n")) != NULL) |
604 |
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); |
605 |
- /* workaround for long NCBI NR lines */ |
606 |
-- while (V->longline && ! feof(V->f)) getline(V); |
607 |
-+ while (V->longline && ! feof(V->f)) get_line(V); |
608 |
- |
609 |
- readLoop(0, endPearson, V); |
610 |
- |
611 |
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) |
612 |
-- getline(V); |
613 |
-+ get_line(V); |
614 |
- } |
615 |
- |
616 |
- |
617 |
-@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V) |
618 |
- |
619 |
- /* make sure we have first line */ |
620 |
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) |
621 |
-- getline(V); |
622 |
-+ get_line(V); |
623 |
- |
624 |
- if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) |
625 |
- { |
626 |
-@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V) |
627 |
- } |
628 |
- |
629 |
- do { |
630 |
-- getline(V); |
631 |
-+ get_line(V); |
632 |
- if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) |
633 |
- { |
634 |
- if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) |
635 |
-@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V) |
636 |
- |
637 |
- /* load next record's ID line */ |
638 |
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) |
639 |
-- getline(V); |
640 |
-+ get_line(V); |
641 |
- } |
642 |
- |
643 |
- |
644 |
-@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V) |
645 |
- { |
646 |
- char *sptr; |
647 |
- |
648 |
-- getline(V); /*s == "seqLen seqid string..."*/ |
649 |
-+ get_line(V); /*s == "seqLen seqid string..."*/ |
650 |
- |
651 |
- if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) |
652 |
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); |
653 |
-@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V) |
654 |
- readLoop(0, endZuker, V); |
655 |
- |
656 |
- while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) |
657 |
-- getline(V); |
658 |
-+ get_line(V); |
659 |
- } |
660 |
- |
661 |
- static void |
662 |
-@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V) |
663 |
- |
664 |
- do { |
665 |
- done = feof(V->f); |
666 |
-- getline(V); |
667 |
-+ get_line(V); |
668 |
- if (! done) addseq(V->sbuffer, V); |
669 |
- } while (!done); |
670 |
- } |
671 |
-@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V) |
672 |
- char *sptr; |
673 |
- int dostruc = FALSE; |
674 |
- |
675 |
-- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); |
676 |
-+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); |
677 |
- |
678 |
- if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) |
679 |
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); |
680 |
-@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V) |
681 |
- /*CONSTCOND*/ |
682 |
- while (1) |
683 |
- { |
684 |
-- getline(V); |
685 |
-+ get_line(V); |
686 |
- if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } |
687 |
- |
688 |
- if (strncmp(V->sbuffer, "SRC ", 4) == 0) |
689 |
-@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V) |
690 |
- while (1) |
691 |
- { |
692 |
- /* sequence line */ |
693 |
-- getline(V); |
694 |
-+ get_line(V); |
695 |
- if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) |
696 |
- break; |
697 |
- addseq(V->sbuffer, V); |
698 |
- /* structure line */ |
699 |
- if (dostruc) |
700 |
- { |
701 |
-- getline(V); |
702 |
-+ get_line(V); |
703 |
- if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } |
704 |
- addstruc(V->sbuffer, V); |
705 |
- } |
706 |
-@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V) |
707 |
- |
708 |
- |
709 |
- while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) |
710 |
-- getline(V); |
711 |
-+ get_line(V); |
712 |
- } |
713 |
- |
714 |
- |
715 |
-@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env) |
716 |
- |
717 |
- /* Load the first line. |
718 |
- */ |
719 |
-- getline(dbfp); |
720 |
-+ get_line(dbfp); |
721 |
- |
722 |
- return dbfp; |
723 |
- } |
724 |
-@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset) |
725 |
- Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); |
726 |
- |
727 |
- fseek(sqfp->f, offset, SEEK_SET); |
728 |
-- getline(sqfp); |
729 |
-+ get_line(sqfp); |
730 |
- } |
731 |
- |
732 |
- |
733 |
-@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp) |
734 |
- if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; |
735 |
- else { |
736 |
- rewind(sqfp->f); |
737 |
-- getline(sqfp); |
738 |
-+ get_line(sqfp); |
739 |
- } |
740 |
- } |
741 |
- |
742 |
-@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) |
743 |
- do { /* skip leading comments on GCG file */ |
744 |
- gotuw = (strstr(V->sbuffer,"..") != NULL); |
745 |
- if (gotuw) readUWGCG(V); |
746 |
-- getline(V); |
747 |
-+ get_line(V); |
748 |
- } while (! feof(V->f)); |
749 |
- break; |
750 |
- |
751 |
|
752 |
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch |
753 |
deleted file mode 100644 |
754 |
index 827ce4cdfa7..00000000000 |
755 |
--- a/sci-biology/wise/files/wise-api.tex.patch |
756 |
+++ /dev/null |
757 |
@@ -1,38 +0,0 @@ |
758 |
---- api.tex.old 2005-03-06 11:31:59.862760952 -0500 |
759 |
-+++ api.tex 2005-03-06 11:42:31.375756384 -0500 |
760 |
-@@ -204,7 +204,7 @@ |
761 |
- \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) |
762 |
- \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins |
763 |
- \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) |
764 |
--\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) |
765 |
-+\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) |
766 |
- \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) |
767 |
- \end{itemize} |
768 |
- |
769 |
-@@ -213,7 +213,7 @@ |
770 |
- \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) |
771 |
- \item Make a protein database from the single protein object (\ref{object_ProteinDB}) |
772 |
- \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) |
773 |
--\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) |
774 |
-+\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) |
775 |
- \item Show the Hscore object using a show function (\ref{object_Hscore}) |
776 |
- \item Retrieve individual protein objects from the database by taking out the |
777 |
- DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object |
778 |
-@@ -232,7 +232,7 @@ |
779 |
- \item Read in a codon table (\ref{object_CodonTable}) |
780 |
- \item Make a random DNA model (\ref{object_RandomModelDNA}) |
781 |
- \item Make an algorithm type (\ref{module_gwrap}) |
782 |
--\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) |
783 |
-+\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) |
784 |
- \item Run the actual algorithm (\ref{module_gwrap}) |
785 |
- \item show the alignment using genedisplay (\ref{module_gwrap}) |
786 |
- \end{itemize} |
787 |
-@@ -5055,7 +5055,7 @@ |
788 |
- Member functions of RandomModel |
789 |
- |
790 |
- \section{sequence\_codon} |
791 |
--\label{module_sequence\_codon} |
792 |
-+\label{module_sequence_codon} |
793 |
- This module only contains factory methods |
794 |
- |
795 |
- \subsection{sequence\_codon factory methods} |
796 |
|
797 |
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env |
798 |
deleted file mode 100644 |
799 |
index 3f781c80833..00000000000 |
800 |
--- a/sci-biology/wise/files/wise-env |
801 |
+++ /dev/null |
802 |
@@ -1 +0,0 @@ |
803 |
-WISECONFIGDIR="/usr/share/wise/wisecfg" |
804 |
|
805 |
diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild |
806 |
index 3d4f0955d84..aa971e0c693 100644 |
807 |
--- a/sci-biology/wise/wise-2.4.0_alpha.ebuild |
808 |
+++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild |
809 |
@@ -7,7 +7,8 @@ inherit eutils toolchain-funcs versionator |
810 |
|
811 |
DESCRIPTION="Intelligent algorithms for DNA searches" |
812 |
HOMEPAGE="http://www.ebi.ac.uk/Wise2/" |
813 |
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" |
814 |
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz |
815 |
+ https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2" |
816 |
|
817 |
LICENSE="BSD" |
818 |
SLOT="0" |
819 |
@@ -25,12 +26,12 @@ S="${WORKDIR}"/${PN}$(delete_version_separator 3) |
820 |
|
821 |
src_prepare() { |
822 |
epatch \ |
823 |
- "${FILESDIR}"/${P}-glibc-2.10.patch \ |
824 |
- "${FILESDIR}"/${P}-cflags.patch |
825 |
+ "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \ |
826 |
+ "${WORKDIR}"/${P}-patchset/${P}-cflags.patch |
827 |
cd "${S}"/docs || die |
828 |
cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die |
829 |
cat wise2api.tex temp.tex apiend.tex > api.tex || die |
830 |
- epatch "${FILESDIR}"/${PN}-api.tex.patch |
831 |
+ epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch |
832 |
} |
833 |
|
834 |
src_compile() { |
835 |
@@ -68,5 +69,5 @@ src_install() { |
836 |
insinto /usr/share/doc/${PF} |
837 |
doins "${S}"/docs/*.ps |
838 |
fi |
839 |
- newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" |
840 |
+ newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file" |
841 |
} |