diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2020-02-29 18:01:47 +0000 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2020-02-29 18:01:47 +0000 |
| commit | ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 (patch) | |
| tree | 9f47ee47c31a0f13f9496879cd88a1042550aa81 /sci-biology/qrna | |
| parent | 53cba99042fa967e2a93da9f8db806fe2d035543 (diff) | |
gentoo (leap year) resync : 29.02.2020
Diffstat (limited to 'sci-biology/qrna')
| -rw-r--r-- | sci-biology/qrna/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch | 357 | ||||
| -rw-r--r-- | sci-biology/qrna/qrna-2.0.3c-r3.ebuild | 15 |
3 files changed, 360 insertions, 16 deletions
diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest index fc5186011f1b..533808de8b3f 100644 --- a/sci-biology/qrna/Manifest +++ b/sci-biology/qrna/Manifest @@ -1,6 +1,6 @@ AUX 26qrna 30 BLAKE2B 07faad9f2143edab789c29f999182e76a87ae82b9e6fca3346fc6391f7581ce3595a70e2432358e527a0a4178078b0e8f881537fe90a069a0b09211476520648 SHA512 ba47d1fe1cba68ca7dce369e814a67cca24339a1ec213d206001b4f87f8939d81c7e59bc285090e5ec2cec05693f560c9c4883cae8f67891f6053d9bc69cc46b AUX qrna-2.0.3c-glibc-2.10.patch 7571 BLAKE2B 3361fa6c31af0fa7f01e3c32bce2a8570df69b06517f9eb46a2f4f249acc972ac15da4fa5b9c1211efeaa91ee7d41f5c5e2392d89ead41252b5f5675826d4c21 SHA512 afa8767baadf99dafbb0ce4fa8b31017f6a12e1eadbcbd41a7e04e571d3f059395356178df3ab28f8c03c10f227123361590357c6ace6256727322ade00228e6 -AUX qrna-2.0.3c-ldflags.patch 1368 BLAKE2B b3f5cee42c370545e348e86627981d4568a84a673faf32d041b0ebbce0e782c8cab1aaa41c2c48f43704886035431c64b035a99b98225363f5ca2d0b8b9c0dc2 SHA512 4b1be14c664056eebb914e8c8223686ef0f345c860bd5aca82dced67b9580a205ef9539c563c0b0c646a9781ed0c58c4cec69d71bceb2c410dc485e9b5881c54 +AUX qrna-2.0.3c-ldflags.patch 18533 BLAKE2B b4901278e494d75895efecf9808e119307ece785437dec6c0776154665205d22cdd95be8526fbdf6f717e45613776b778b6c4a4f7561b3ec4e57ffda1547212e SHA512 6090e90d1723001dcda9a613bb13387bb6cf1b33c1692d4ea40efd1e14bce792779bf6b9acf3eed964c9432f49d2325e4bf910c87cc076e2e7a9329b4f9371d9 DIST qrna-2.0.3c.tar.bz2 6423705 BLAKE2B 42bb2f03bac4034da9bcdedcd7c09ce7d1892ceb14d5682745d77c7575a84ae1a6a598406895be2a844ceaffee045ec6357ad08cc0d67a1312458d11b6540fda SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 -EBUILD qrna-2.0.3c-r3.ebuild 1114 BLAKE2B 737bf8541a3812727d8d2c8adba527cc259b52fa88ed411c56c91a5783b3bc41d001da59b67ae79f02df48fda79859fae352a00dae452de291f1a7bce93676cf SHA512 008cb677ee7548fbae56f87e0394f135cc89c9811ad598157cb1b2ce2f708a715bb8a9b841b5348ef2647dd4a488905960d0a6448d5c13fcd05be61361c4de37 +EBUILD qrna-2.0.3c-r3.ebuild 950 BLAKE2B adf9ed2e0efbdc1324e7ab68366f4bea99a1e27192d6d7eebff579a74c647af45b2150649347c581547bf78e266ebcde909ced51eeca63ade688007f51c065c6 SHA512 a59e67d3e608b1b441fd4f8a80bcdeb89431372406d149bb0df84a375a376e4b5b7d4bc74771b0e48daebdf412b63b04e3e83bcc32a583f1436fb30a6f320baf MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch index d03f650dd39e..17ca27e6da5a 100644 --- a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch +++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch @@ -1,13 +1,156 @@ -diff --git a/src/Makefile b/src/Makefile -index 1d1631b..4fa3af9 100644 +--- a/squid/Makefile ++++ b/squid/Makefile +@@ -19,7 +19,6 @@ + # On an Alliant, use fxc. + # + #CC = cc +-CC = gcc + #CC = fxc + + ## Any special compiler flags you want. +@@ -37,7 +36,6 @@ + # for instance. If the code builds cleanly but seg faults, try + # rebuilding without optimization. + # +-CFLAGS = -O + #CFLAGS = -g + #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# + +@@ -47,8 +45,6 @@ + # Don't worry. The Makefile tests for ranlib existence and will work + # fine on SGIs even if RANLIB is set. + # +-AR = ar rcv +-RANLIB = ranlib + + ## Machine specific definitions + # +@@ -108,41 +104,41 @@ + all: $(LIBTARGET) + + alistat: $(OBJ) alistat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o alistat $(OBJ) alistat_main.o $(LIBS) + + compalign: $(OBJ) compalign_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compalign $(OBJ) compalign_main.o $(LIBS) + + compstruct: $(OBJ) compstruct_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o compstruct $(OBJ) compstruct_main.o $(LIBS) + + getseq: $(OBJ) getseq_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o getseq $(OBJ) getseq_main.o $(LIBS) + + reformat: $(OBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o reformat $(OBJ) reformat_main.o $(LIBS) + + revcomp: $(OBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o revcomp $(OBJ) revcomp_main.o $(LIBS) + + seqstat: $(OBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqstat_main.o $(LIBS) + + seqsplit: $(OBJ) seqsplit_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o seqstat $(OBJ) seqsplit_main.o $(LIBS) + + shuffle: $(OBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o shuffle $(OBJ) shuffle_main.o $(LIBS) + + translate: $(OBJ) translate_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o translate $(OBJ) translate_main.o $(LIBS) + + weight: $(OBJ) weight_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o weight $(OBJ) weight_main.o $(LIBS) + + + $(LIBTARGET): $(OBJ) +- $(AR) $(LIBTARGET) $(OBJ) ++ $(AR) rcv $(LIBTARGET) $(OBJ) + -if test -x /bin/ranlib; then /bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x /usr/bin/ranlib; then /usr/bin/ranlib $(LIBTARGET); else exit 0; fi + -if test -x $(RANLIB); then $(RANLIB) $(LIBTARGET); else exit 0; fi +@@ -182,4 +178,4 @@ + etags -t $(SRC) $(HDRS) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< +--- a/squid02/Makefile ++++ b/squid02/Makefile +@@ -27,8 +27,6 @@ + + ## your compiler and compiler flags + # +-CC = gcc +-CFLAGS = -g -O2 + + ## other defined flags for machine-specific stuff + # +@@ -37,8 +35,6 @@ + + ## Archiver command + # +-AR = ar rcv +-RANLIB = ranlib + + ## instructions for installing man pages + # +@@ -158,10 +154,10 @@ + all: version.h $(PROGS) libsquid.a + + $(PROGS): %: %_main.o version.h $(OBJS) +- $(CC) $(CFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) $(PVMLIBDIR) -o $@ $@_main.o $(OBJS) $(PVMLIBS) $(LIBS) + + .c.o: +- $(CC) $(CFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(PVMFLAG) $(PVMINCDIR) $(MDEFS) -c $< + ################################################################ + + +@@ -172,7 +168,7 @@ + module: libsquid.a + + libsquid.a: version.h $(OBJS) +- $(AR) libsquid.a $(OBJS) ++ $(AR) rcv libsquid.a $(OBJS) + $(RANLIB) libsquid.a + chmod 644 libsquid.a + ################################################################# --- a/src/Makefile +++ b/src/Makefile -@@ -131,17 +131,17 @@ DEMOS = +@@ -21,7 +21,6 @@ + SQUIDSRCDIR02 = ../squid02 + + ## your compiler +-CC = gcc + #CC = cc + + ## any special compiler flags you want +@@ -30,7 +29,6 @@ + #CFLAGS = -g -Wall -pedantic + #CFLAGS = -TARG:exc_max + #CFLAGS = -g -fullwarn -wlint,-fviah +-CFLAGS = -O + #CFLAGS = -p # profiling # + #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# + +@@ -131,145 +129,145 @@ all: $(PROGS) main: $(OBJ) main.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) cfgbuild: $(OBJ) cfgbuild.o - $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) @@ -25,4 +168,208 @@ index 1d1631b..4fa3af9 100644 + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) main.o: ../src/main.c - $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgbuild.o: ../src/cfgbuild.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna.o: ../src/eqrna.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + eqrna_sample.o: ../src/eqrna_sample.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + shuffle.o: ../src/shuffle.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat_main.o: ../src/rnamat_main.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + + cfgio.o: ../src/cfgio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgmodel.o: ../src/cfgmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + cfgparse.o: ../src/cfgparse.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codcreatealign.o: ../src/codcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddp.o: ../src/coddp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + coddpscanfast.o: ../src/coddpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codmodel.o: ../src/codmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codon.o: ../src/codon.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + codscorealign.o: ../src/codscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_math.o: ../src/er_math.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + er_vectop.o: ../src/er_vectop.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + evd.o: ../src/evd.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolcodmodel.o: ../src/evolcodmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolemissions.o: ../src/evolemissions.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolmisc.o: ../src/evolmisc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolnullmodel.o: ../src/evolnullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolothmodel.o: ../src/evolothmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolqrnaversion.o: ../src/evolqrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodels.o: ../src/evolscorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolscorewithmodelscanfast.o: ../src/evolscorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolriboprob.o: ../src/evolriboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadp.o: ../src/evolrnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnadpscanfast.o: ../src/evolrnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnamodel.o: ../src/evolrnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolrnascorealign.o: ../src/evolrnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + evolve.o: ../src/evolve.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + globals.o: ../src/globals.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + hexamer.o: ../src/hexamer.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + matrix.o: ../src/matrix.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + misc.o: ../src/misc.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nrnscfg.o: ../src/nrnscfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + nstack.o: ../src/nstack.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + nullmodel.o: ../src/nullmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othcreatealign.o: ../src/othcreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdp.o: ../src/othdp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othdpscanfast.o: ../src/othdpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othmodel.o: ../src/othmodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + othscorealign.o: ../src/othscorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + posterior.o: ../src/posterior.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + qrnaversion.o: ../src/qrnaversion.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + riboprob.o: ../src/riboprob.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnacreatealign.o: ../src/rnacreatealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadp.o: ../src/rnadp.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnadpscanfast.o: ../src/rnadpscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaio.o: ../src/rnaio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnamat.o: ../src/rnamat.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR02) -c $? + rnamodel.o: ../src/rnamodel.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnaoutput.o: ../src/rnaoutput.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascorealign.o: ../src/rnascorealign.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfg.o: ../src/rnascfg.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + rnascfgscanfast.o: ../src/rnascfgscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodels.o: ../src/scorewithmodels.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + scorewithmodelscanfast.o: ../src/scorewithmodelscanfast.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + seqio.o: ../src/seqio.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + trace.o: ../src/trace.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + traceSCFG.o: ../src/traceSCFG.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + tying.o: ../src/tying.c +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? + + + install: $(PROGS) +@@ -313,10 +311,10 @@ + /usr/lib/lint/llib-lm.ln + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + .m.o: +- $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $< + + + diff --git a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild index 5c580a24d2a3..34b59e9fb0a3 100644 --- a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild +++ b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -12,7 +12,6 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" RDEPEND=" dev-lang/perl @@ -26,15 +25,13 @@ PATCHES=( src_prepare() { default - sed \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -e "/^AR/s:ar:$(tc-getAR):g" \ - -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \ - -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \ - -i {src,squid,squid02}/Makefile || die rm -v squid*/*.a || die } +src_configure() { + tc-export AR CC RANLIB +} + src_compile() { local d for d in squid squid02 src; do |