* [gentoo-commits] repo/gentoo:master commit in: sci-biology/qrna/, sci-biology/qrna/files/
@ 2024-03-21 5:58 Sam James
0 siblings, 0 replies; 2+ messages in thread
From: Sam James @ 2024-03-21 5:58 UTC (permalink / raw
To: gentoo-commits
commit: c19c464def01a163fc04351c151a98d4048095e3
Author: Eli Schwartz <eschwartz93 <AT> gmail <DOT> com>
AuthorDate: Thu Mar 21 00:25:02 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu Mar 21 05:57:37 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c19c464d
sci-biology/qrna: add 2.0.4
This is the 2006 edition of the software. It has a bunch of useful
fixes:
- it fixes Modern C porting issues
- it fixes LTO errors
- it incorporates the glibc-2.10 patch
just by upgrading! It's about time we upgrade, since it is 18 years
later.
Along the way we fix up the ebuild a bit:
- bump to EAPI 8
- acquire an actual SRC_URI, not just the gentoo mirror
- update the homepage along with the SRC_URI. The original homepage is
dead, and the domain redirects to a new domain (whence comes the new
distfile).
It has some shortcomings too:
- the distfile comes with free .svn directories, which have to be
pruned.
- the distfile comes without the 80mb demos
To solve this, we use the old distfile (which I think only exists on
Gentoo's mirror network) and gate it behind a USE=examples flag, in case
anyone needs them.
Closes: https://bugs.gentoo.org/862285
Closes: https://bugs.gentoo.org/884283
Signed-off-by: Eli Schwartz <eschwartz93 <AT> gmail.com>
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/qrna/Manifest | 1 +
sci-biology/qrna/files/qrna-2.0.4-ldflags.patch | 381 ++++++++++++++++++++++++
sci-biology/qrna/qrna-2.0.4.ebuild | 61 ++++
3 files changed, 443 insertions(+)
diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest
index aa10390b4217..9532795cb306 100644
--- a/sci-biology/qrna/Manifest
+++ b/sci-biology/qrna/Manifest
@@ -1 +1,2 @@
DIST qrna-2.0.3c.tar.bz2 6423705 BLAKE2B 42bb2f03bac4034da9bcdedcd7c09ce7d1892ceb14d5682745d77c7575a84ae1a6a598406895be2a844ceaffee045ec6357ad08cc0d67a1312458d11b6540fda SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5
+DIST qrna-2.0.4.tar.gz 3220929 BLAKE2B 77f1272ad9952a3b47142fe996e3838bf13d845e19753e73ad941c2a055e7cc1a714a41543097120d5e96aaa8d5d0394e7083413599f60dac21261b2e4071fd3 SHA512 9d2d697d537f9fb0dac374de1b80f6862630cea0bd7cd68f8c3fcf97457d393d2e38e709aac674f4e50d437d5ce11f0bf527c705c2bd28c3017894c11ea17222
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
+}
^ permalink raw reply related [flat|nested] 2+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/qrna/, sci-biology/qrna/files/
@ 2020-02-23 11:52 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2020-02-23 11:52 UTC (permalink / raw
To: gentoo-commits
commit: b24fab79ca7863993080b5fafd4ce414ff132c73
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 23 11:51:59 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 23 11:51:59 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b24fab79
sci-biology/qrna: Port to EAPI 7
Closes: https://bugs.gentoo.org/710554
Package-Manager: Portage-2.3.89, Repoman-2.3.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch | 357 ++++++++++++++++++++++-
sci-biology/qrna/qrna-2.0.3c-r3.ebuild | 15 +-
2 files changed, 358 insertions(+), 14 deletions(-)
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 d03f650dd39..17ca27e6da5 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 $<
+
+
+
diff --git a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
index 5c580a24d2a..34b59e9fb0a 100644
--- a/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
+++ b/sci-biology/qrna/qrna-2.0.3c-r3.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit toolchain-funcs
@@ -12,7 +12,6 @@ SRC_URI="mirror://gentoo/${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
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2024-03-21 5:58 [gentoo-commits] repo/gentoo:master commit in: sci-biology/qrna/, sci-biology/qrna/files/ Sam James
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2020-02-23 11:52 David Seifert
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