From 3faa6ebe0068b432ee5a9390c47ceca068ea7fe9 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Thu, 21 Mar 2024 07:00:13 +0000 Subject: gentoo auto-resync : 21:03:2024 - 07:00:13 --- sci-biology/Manifest.gz | Bin 19328 -> 19332 bytes sci-biology/qrna/Manifest | 3 + sci-biology/qrna/files/qrna-2.0.4-ldflags.patch | 381 ++++++++++++++++++++++++ sci-biology/qrna/qrna-2.0.4.ebuild | 61 ++++ 4 files changed, 445 insertions(+) create mode 100644 sci-biology/qrna/files/qrna-2.0.4-ldflags.patch create mode 100644 sci-biology/qrna/qrna-2.0.4.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index fc6ee0836d4a..ca357d460b60 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest index 0a948e3e7f83..a7152b613a4f 100644 --- a/sci-biology/qrna/Manifest +++ b/sci-biology/qrna/Manifest @@ -1,6 +1,9 @@ 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 18533 BLAKE2B b4901278e494d75895efecf9808e119307ece785437dec6c0776154665205d22cdd95be8526fbdf6f717e45613776b778b6c4a4f7561b3ec4e57ffda1547212e SHA512 6090e90d1723001dcda9a613bb13387bb6cf1b33c1692d4ea40efd1e14bce792779bf6b9acf3eed964c9432f49d2325e4bf910c87cc076e2e7a9329b4f9371d9 +AUX qrna-2.0.4-ldflags.patch 19022 BLAKE2B 0c360b47e0bec5e73e74b9a64a216326cadfaaaf55476f1e02d29230a005b2046ec313bbe43f3ee1e5d15dda1cfec7b144337480b689bdd53cd2c1552e43648e SHA512 5a1b9fe985d8ce5fc6e32362ffd92ef277e771e610981c58009e64bf9cc4c1994d974820671185646fd051396769a096fabeb344db6d29e310a71a8f8a8e4561 DIST qrna-2.0.3c.tar.bz2 6423705 BLAKE2B 42bb2f03bac4034da9bcdedcd7c09ce7d1892ceb14d5682745d77c7575a84ae1a6a598406895be2a844ceaffee045ec6357ad08cc0d67a1312458d11b6540fda SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 +DIST qrna-2.0.4.tar.gz 3220929 BLAKE2B 77f1272ad9952a3b47142fe996e3838bf13d845e19753e73ad941c2a055e7cc1a714a41543097120d5e96aaa8d5d0394e7083413599f60dac21261b2e4071fd3 SHA512 9d2d697d537f9fb0dac374de1b80f6862630cea0bd7cd68f8c3fcf97457d393d2e38e709aac674f4e50d437d5ce11f0bf527c705c2bd28c3017894c11ea17222 EBUILD qrna-2.0.3c-r3.ebuild 950 BLAKE2B adf9ed2e0efbdc1324e7ab68366f4bea99a1e27192d6d7eebff579a74c647af45b2150649347c581547bf78e266ebcde909ced51eeca63ade688007f51c065c6 SHA512 a59e67d3e608b1b441fd4f8a80bcdeb89431372406d149bb0df84a375a376e4b5b7d4bc74771b0e48daebdf412b63b04e3e83bcc32a583f1436fb30a6f320baf +EBUILD qrna-2.0.4.ebuild 1084 BLAKE2B 8346e859532130791ff7ec75e6be36a90f6bb0ac4d62790a1b2fcc0a8c30264ed58d9dca9147e498fbcac6aad92f198e06c4e6fec755e69ef8cf1650509e48b7 SHA512 422e6fbb20b46ea0fb839ebb6f02b26af38ba4771021484b6d37aebd2403f2094fb929eb65226de6e7b88c2d1c4f9c2af817425e18bcc78f6841dff45e02ad44 MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f diff --git a/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch new file mode 100644 index 000000000000..c53b56b0e935 --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.4-ldflags.patch @@ -0,0 +1,381 @@ +diff --git a/squid/Makefile b/squid/Makefile +index fafab4c..8c329b3 100644 +--- a/squid/Makefile ++++ b/squid/Makefile +@@ -19,7 +19,6 @@ MANDIR = $(HOME)/man + # On an Alliant, use fxc. + # + #CC = cc +-CC = gcc + #CC = fxc + + ## Any special compiler flags you want. +@@ -37,7 +36,6 @@ CC = gcc + # for instance. If the code builds cleanly but seg faults, try + # rebuilding without optimization. + # +-CFLAGS = -O -m32 + #CFLAGS = -g + #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# + +@@ -47,8 +45,6 @@ CFLAGS = -O -m32 + # 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 @@ DIST = $(SRC) $(HDRS) $(READMES) Makefile + 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 @@ tags: + etags -t $(SRC) $(HDRS) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< +diff --git a/squid02/Makefile b/squid02/Makefile +index d32240f..757e0dd 100644 +--- a/squid02/Makefile ++++ b/squid02/Makefile +@@ -27,8 +27,6 @@ SCRIPTDIR = ${exec_prefix}/bin + + ## your compiler and compiler flags + # +-CC = gcc +-CFLAGS = -g -O2 -m32 + + ## other defined flags for machine-specific stuff + # +@@ -37,8 +35,6 @@ LIBS = -lm + + ## Archiver command + # +-AR = ar rcv +-RANLIB = ranlib + + ## instructions for installing man pages + # +@@ -158,10 +154,10 @@ OBJS = a2m.o\ + 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 @@ $(PROGS): %: %_main.o version.h $(OBJS) + module: libsquid.a + + libsquid.a: version.h $(OBJS) +- $(AR) libsquid.a $(OBJS) ++ $(AR) rcv libsquid.a $(OBJS) + $(RANLIB) libsquid.a + chmod 644 libsquid.a + ################################################################# +diff --git a/src/Makefile b/src/Makefile +index d93182b..35c8b3d 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -21,7 +21,6 @@ SQUIDDIR02 = ../squid02 + SQUIDSRCDIR02 = ../squid02 + + ## your compiler +-CC = gcc + #CC = cc + + ## any special compiler flags you want +@@ -30,7 +29,6 @@ CC = gcc + #CFLAGS = -g -Wall -pedantic + #CFLAGS = -TARG:exc_max + #CFLAGS = -g -fullwarn -wlint,-fviah +-CFLAGS = -O -m32 + #CFLAGS = -p # profiling # + #CFLAGS = -64 -Ofast=ip27 #specific warhorse compiler# + +@@ -131,145 +129,145 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -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) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.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 @@ lint: + /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-2.0.4.ebuild b/sci-biology/qrna/qrna-2.0.4.ebuild new file mode 100644 index 000000000000..58e2045e8fc2 --- /dev/null +++ b/sci-biology/qrna/qrna-2.0.4.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs vcs-clean + +DESCRIPTION="Prototype ncRNA genefinder" +HOMEPAGE="http://eddylab.org/software.html" +SRC_URI=" + http://eddylab.org/software/qrna/qrna.tar.gz -> ${P}.tar.gz + examples? ( mirror://gentoo/qrna-2.0.3c.tar.bz2 ) +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +RDEPEND=" + dev-lang/perl + sci-biology/hmmer:2" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-ldflags.patch +) + +src_prepare() { + default + esvn_clean + rm -v squid*/*.a || die +} + +src_configure() { + tc-export AR CC RANLIB +} + +src_compile() { + local d + for d in squid squid02 src; do + emake -C ${d} + done +} + +src_install() { + dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/* + + newdoc 00README README + dodoc -r documentation/. + + insinto /usr/share/${PN}/data + doins -r lib/. + if use examples; then + insinto /usr/share/${PN}/demos + doins -r "${WORKDIR}"/qrna-2.0.3c/Demos/. + fi + + # Sets the path to the QRNA data files + doenvd "${FILESDIR}"/26qrna +} -- cgit v1.2.3