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commit: b24fab79ca7863993080b5fafd4ce414ff132c73 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Feb 23 11:51:59 2020 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Feb 23 11:51:59 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b24fab79 |
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|
| 8 |
sci-biology/qrna: Port to EAPI 7 |
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|
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Closes: https://bugs.gentoo.org/710554 |
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Package-Manager: Portage-2.3.89, Repoman-2.3.20 |
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch | 357 ++++++++++++++++++++++- |
| 15 |
sci-biology/qrna/qrna-2.0.3c-r3.ebuild | 15 +- |
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2 files changed, 358 insertions(+), 14 deletions(-) |
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|
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diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch |
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index d03f650dd39..17ca27e6da5 100644 |
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--- a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch |
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+++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch |
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@@ -1,13 +1,156 @@ |
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-diff --git a/src/Makefile b/src/Makefile |
| 24 |
-index 1d1631b..4fa3af9 100644 |
| 25 |
+--- a/squid/Makefile |
| 26 |
++++ b/squid/Makefile |
| 27 |
+@@ -19,7 +19,6 @@ |
| 28 |
+ # On an Alliant, use fxc. |
| 29 |
+ # |
| 30 |
+ #CC = cc |
| 31 |
+-CC = gcc |
| 32 |
+ #CC = fxc |
| 33 |
+ |
| 34 |
+ ## Any special compiler flags you want. |
| 35 |
+@@ -37,7 +36,6 @@ |
| 36 |
+ # for instance. If the code builds cleanly but seg faults, try |
| 37 |
+ # rebuilding without optimization. |
| 38 |
+ # |
| 39 |
+-CFLAGS = -O |
| 40 |
+ #CFLAGS = -g |
| 41 |
+ #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# |
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+ |
| 43 |
+@@ -47,8 +45,6 @@ |
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+ # Don't worry. The Makefile tests for ranlib existence and will work |
| 45 |
+ # fine on SGIs even if RANLIB is set. |
| 46 |
+ # |
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+-AR = ar rcv |
| 48 |
+-RANLIB = ranlib |
| 49 |
+ |
| 50 |
+ ## Machine specific definitions |
| 51 |
+ # |
| 52 |
+@@ -108,41 +104,41 @@ |
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+ all: $(LIBTARGET) |
| 54 |
+ |
| 55 |
+ alistat: $(OBJ) alistat_main.o |
| 56 |
+- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) |
| 57 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) |
| 58 |
+ |
| 59 |
+ compalign: $(OBJ) compalign_main.o |
| 60 |
+- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) |
| 61 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) |
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+ |
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+ compstruct: $(OBJ) compstruct_main.o |
| 64 |
+- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) |
| 65 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) |
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+ |
| 67 |
+ getseq: $(OBJ) getseq_main.o |
| 68 |
+- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) |
| 69 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) |
| 70 |
+ |
| 71 |
+ reformat: $(OBJ) reformat_main.o |
| 72 |
+- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) |
| 73 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) |
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+ |
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+ revcomp: $(OBJ) revcomp_main.o |
| 76 |
+- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) |
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++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) |
| 78 |
+ |
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+ seqstat: $(OBJ) seqstat_main.o |
| 80 |
+- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) |
| 81 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) |
| 82 |
+ |
| 83 |
+ seqsplit: $(OBJ) seqsplit_main.o |
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+- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) |
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++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) |
| 86 |
+ |
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+ shuffle: $(OBJ) shuffle_main.o |
| 88 |
+- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) |
| 89 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) |
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+ |
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+ translate: $(OBJ) translate_main.o |
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+- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) |
| 93 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) |
| 94 |
+ |
| 95 |
+ weight: $(OBJ) weight_main.o |
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+- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) |
| 97 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) |
| 98 |
+ |
| 99 |
+ |
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+ $(LIBTARGET): $(OBJ) |
| 101 |
+- $(AR) $(LIBTARGET) $(OBJ) |
| 102 |
++ $(AR) rcv $(LIBTARGET) $(OBJ) |
| 103 |
+ -if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi |
| 104 |
+ -if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi |
| 105 |
+ -if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi |
| 106 |
+@@ -182,4 +178,4 @@ |
| 107 |
+ etags -t $(SRC) $(HDRS) |
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+ |
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+ .c.o: |
| 110 |
+- $(CC) $(CFLAGS) $(MDEFS) -c $< |
| 111 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< |
| 112 |
+--- a/squid02/Makefile |
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++++ b/squid02/Makefile |
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+@@ -27,8 +27,6 @@ |
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+ |
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+ ## your compiler and compiler flags |
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+ # |
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+-CC = gcc |
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+-CFLAGS = -g -O2 |
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+ |
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+ ## other defined flags for machine-specific stuff |
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+ # |
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+@@ -37,8 +35,6 @@ |
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+ |
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+ ## Archiver command |
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+ # |
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+-AR = ar rcv |
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+-RANLIB = ranlib |
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+ |
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+ ## instructions for installing man pages |
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+ # |
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+@@ -158,10 +154,10 @@ |
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+ all: version.h $(PROGS) libsquid.a |
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+ |
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+ $(PROGS): %: %_main.o version.h $(OBJS) |
| 136 |
+- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) |
| 137 |
++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) |
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+ |
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+ .c.o: |
| 140 |
+- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< |
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++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< |
| 142 |
+ ################################################################ |
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+ |
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+ |
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+@@ -172,7 +168,7 @@ |
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+ module: libsquid.a |
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+ |
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+ libsquid.a: version.h $(OBJS) |
| 149 |
+- $(AR) libsquid.a $(OBJS) |
| 150 |
++ $(AR) rcv libsquid.a $(OBJS) |
| 151 |
+ $(RANLIB) libsquid.a |
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+ chmod 644 libsquid.a |
| 153 |
+ ################################################################# |
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--- a/src/Makefile |
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+++ b/src/Makefile |
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-@@ -131,17 +131,17 @@ DEMOS = |
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+@@ -21,7 +21,6 @@ |
| 158 |
+ SQUIDSRCDIR02 = ../squid02 |
| 159 |
+ |
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+ ## your compiler |
| 161 |
+-CC = gcc |
| 162 |
+ #CC = cc |
| 163 |
+ |
| 164 |
+ ## any special compiler flags you want |
| 165 |
+@@ -30,7 +29,6 @@ |
| 166 |
+ #CFLAGS = -g -Wall -pedantic |
| 167 |
+ #CFLAGS = -TARG:exc_max |
| 168 |
+ #CFLAGS = -g -fullwarn -wlint,-fviah |
| 169 |
+-CFLAGS = -O |
| 170 |
+ #CFLAGS = -p # profiling # |
| 171 |
+ #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# |
| 172 |
+ |
| 173 |
+@@ -131,145 +129,145 @@ |
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all: $(PROGS) |
| 175 |
|
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main: $(OBJ) main.o |
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- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) |
| 178 |
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) |
| 179 |
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) |
| 180 |
cfgbuild: $(OBJ) cfgbuild.o |
| 181 |
- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) |
| 182 |
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) |
| 183 |
@@ -25,4 +168,208 @@ index 1d1631b..4fa3af9 100644 |
| 184 |
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) |
| 185 |
|
| 186 |
main.o: ../src/main.c |
| 187 |
- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 188 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 189 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 190 |
+ cfgbuild.o: ../src/cfgbuild.c |
| 191 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 192 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 193 |
+ eqrna.o: ../src/eqrna.c |
| 194 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 195 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 196 |
+ eqrna_sample.o: ../src/eqrna_sample.c |
| 197 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 198 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 199 |
+ shuffle.o: ../src/shuffle.c |
| 200 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 201 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 202 |
+ rnamat_main.o: ../src/rnamat_main.c |
| 203 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 204 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 205 |
+ |
| 206 |
+ cfgio.o: ../src/cfgio.c |
| 207 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 208 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 209 |
+ cfgmodel.o: ../src/cfgmodel.c |
| 210 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 211 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 212 |
+ cfgparse.o: ../src/cfgparse.c |
| 213 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 214 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 215 |
+ codcreatealign.o: ../src/codcreatealign.c |
| 216 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 217 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 218 |
+ coddp.o: ../src/coddp.c |
| 219 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 220 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 221 |
+ coddpscanfast.o: ../src/coddpscanfast.c |
| 222 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 223 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 224 |
+ codmodel.o: ../src/codmodel.c |
| 225 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 226 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 227 |
+ codon.o: ../src/codon.c |
| 228 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 229 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 230 |
+ codscorealign.o: ../src/codscorealign.c |
| 231 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 232 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 233 |
+ er_math.o: ../src/er_math.c |
| 234 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 235 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 236 |
+ er_vectop.o: ../src/er_vectop.c |
| 237 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 238 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 239 |
+ evd.o: ../src/evd.c |
| 240 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 241 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 242 |
+ evolcodmodel.o: ../src/evolcodmodel.c |
| 243 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 244 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 245 |
+ evolemissions.o: ../src/evolemissions.c |
| 246 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 247 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 248 |
+ evolmisc.o: ../src/evolmisc.c |
| 249 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 250 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 251 |
+ evolnullmodel.o: ../src/evolnullmodel.c |
| 252 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 253 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 254 |
+ evolothmodel.o: ../src/evolothmodel.c |
| 255 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 256 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 257 |
+ evolqrnaversion.o: ../src/evolqrnaversion.c |
| 258 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 259 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 260 |
+ evolscorewithmodels.o: ../src/evolscorewithmodels.c |
| 261 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 262 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 263 |
+ evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c |
| 264 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 265 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 266 |
+ evolriboprob.o: ../src/evolriboprob.c |
| 267 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 268 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 269 |
+ evolrnadp.o: ../src/evolrnadp.c |
| 270 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 271 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 272 |
+ evolrnadpscanfast.o: ../src/evolrnadpscanfast.c |
| 273 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 274 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 275 |
+ evolrnamodel.o: ../src/evolrnamodel.c |
| 276 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 277 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 278 |
+ evolrnascorealign.o: ../src/evolrnascorealign.c |
| 279 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 280 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 281 |
+ evolve.o: ../src/evolve.c |
| 282 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 283 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 284 |
+ globals.o: ../src/globals.c |
| 285 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 286 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 287 |
+ hexamer.o: ../src/hexamer.c |
| 288 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 289 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 290 |
+ matrix.o: ../src/matrix.c |
| 291 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 292 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 293 |
+ misc.o: ../src/misc.c |
| 294 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 295 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 296 |
+ nrnscfg.o: ../src/nrnscfg.c |
| 297 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 298 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 299 |
+ nstack.o: ../src/nstack.c |
| 300 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 301 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 302 |
+ nullmodel.o: ../src/nullmodel.c |
| 303 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 304 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 305 |
+ othcreatealign.o: ../src/othcreatealign.c |
| 306 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 307 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 308 |
+ othdp.o: ../src/othdp.c |
| 309 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 310 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 311 |
+ othdpscanfast.o: ../src/othdpscanfast.c |
| 312 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 313 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 314 |
+ othmodel.o: ../src/othmodel.c |
| 315 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 316 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 317 |
+ othscorealign.o: ../src/othscorealign.c |
| 318 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 319 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 320 |
+ posterior.o: ../src/posterior.c |
| 321 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 322 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 323 |
+ qrnaversion.o: ../src/qrnaversion.c |
| 324 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 325 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 326 |
+ riboprob.o: ../src/riboprob.c |
| 327 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 328 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 329 |
+ rnacreatealign.o: ../src/rnacreatealign.c |
| 330 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 331 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 332 |
+ rnadp.o: ../src/rnadp.c |
| 333 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 334 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 335 |
+ rnadpscanfast.o: ../src/rnadpscanfast.c |
| 336 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 337 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 338 |
+ rnaio.o: ../src/rnaio.c |
| 339 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 340 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 341 |
+ rnamat.o: ../src/rnamat.c |
| 342 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 343 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? |
| 344 |
+ rnamodel.o: ../src/rnamodel.c |
| 345 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 346 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 347 |
+ rnaoutput.o: ../src/rnaoutput.c |
| 348 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 349 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 350 |
+ rnascorealign.o: ../src/rnascorealign.c |
| 351 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 352 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 353 |
+ rnascfg.o: ../src/rnascfg.c |
| 354 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 355 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 356 |
+ rnascfgscanfast.o: ../src/rnascfgscanfast.c |
| 357 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 358 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 359 |
+ scorewithmodels.o: ../src/scorewithmodels.c |
| 360 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 361 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 362 |
+ scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c |
| 363 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 364 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 365 |
+ seqio.o: ../src/seqio.c |
| 366 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 367 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 368 |
+ trace.o: ../src/trace.c |
| 369 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 370 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 371 |
+ traceSCFG.o: ../src/traceSCFG.c |
| 372 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 373 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 374 |
+ tying.o: ../src/tying.c |
| 375 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 376 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? |
| 377 |
+ |
| 378 |
+ |
| 379 |
+ install: $(PROGS) |
| 380 |
+@@ -313,10 +311,10 @@ |
| 381 |
+ /usr/lib/lint/llib-lm.ln |
| 382 |
+ |
| 383 |
+ .c.o: |
| 384 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< |
| 385 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< |
| 386 |
+ |
| 387 |
+ .m.o: |
| 388 |
+- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< |
| 389 |
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< |
| 390 |
+ |
| 391 |
+ |
| 392 |
+ |
| 393 |
|
| 394 |
diff --git a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild |
| 395 |
index 5c580a24d2a..34b59e9fb0a 100644 |
| 396 |
--- a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild |
| 397 |
+++ b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild |
| 398 |
@@ -1,7 +1,7 @@ |
| 399 |
-# Copyright 1999-2017 Gentoo Foundation |
| 400 |
+# Copyright 1999-2020 Gentoo Authors |
| 401 |
# Distributed under the terms of the GNU General Public License v2 |
| 402 |
|
| 403 |
-EAPI=6 |
| 404 |
+EAPI=7 |
| 405 |
|
| 406 |
inherit toolchain-funcs |
| 407 |
|
| 408 |
@@ -12,7 +12,6 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2" |
| 409 |
LICENSE="GPL-2" |
| 410 |
SLOT="0" |
| 411 |
KEYWORDS="~amd64 ~x86" |
| 412 |
-IUSE="" |
| 413 |
|
| 414 |
RDEPEND=" |
| 415 |
dev-lang/perl |
| 416 |
@@ -26,15 +25,13 @@ PATCHES=( |
| 417 |
|
| 418 |
src_prepare() { |
| 419 |
default |
| 420 |
- sed \ |
| 421 |
- -e "s:^CC.*:CC = $(tc-getCC):" \ |
| 422 |
- -e "/^AR/s:ar:$(tc-getAR):g" \ |
| 423 |
- -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \ |
| 424 |
- -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \ |
| 425 |
- -i {src,squid,squid02}/Makefile || die |
| 426 |
rm -v squid*/*.a || die |
| 427 |
} |
| 428 |
|
| 429 |
+src_configure() { |
| 430 |
+ tc-export AR CC RANLIB |
| 431 |
+} |
| 432 |
+ |
| 433 |
src_compile() { |
| 434 |
local d |
| 435 |
for d in squid squid02 src; do |
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