From 90c88731bd036e5698b281fbc0a5f3aa4c9983ac Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 29 Jun 2020 11:38:31 +0100 Subject: gentoo resync : 29.06.2020 --- sci-biology/infernal/Manifest | 6 +- .../files/infernal-1.0.2-fix-build-system.patch | 135 +++++++++++++++++++++ .../infernal/files/infernal-1.0.2-ldflags.patch | 15 --- .../files/infernal-1.0.2-parallel-build.patch | 31 ----- .../files/infernal-1.0.2-respect-DESTDIR.patch | 16 --- sci-biology/infernal/infernal-1.0.2-r1.ebuild | 13 +- 6 files changed, 144 insertions(+), 72 deletions(-) create mode 100644 sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch delete mode 100644 sci-biology/infernal/files/infernal-1.0.2-ldflags.patch delete mode 100644 sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch delete mode 100644 sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch (limited to 'sci-biology/infernal') diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest index a83edfa3624a..54dff0d8887c 100644 --- a/sci-biology/infernal/Manifest +++ b/sci-biology/infernal/Manifest @@ -1,8 +1,6 @@ -AUX infernal-1.0.2-ldflags.patch 444 BLAKE2B 287cac3afc2898d51e5dbf82b64e793dc5decfa134365e91f1ea599df63ca736ec979063a64f2ff3a52bd5213a836a0f2b9875b5142c4a8245403261d5b382b1 SHA512 95f953bbf57a78f40df51bbfdab62e715905aa2bc57d4ca75e380c81d34c88d0177e6fe51933c908bf6e6f513b8c38ffeeb7c8f1802773c7c9773a36388b81d0 +AUX infernal-1.0.2-fix-build-system.patch 3142 BLAKE2B e5869c089b158cb8c22bff849e2a6c22a01d485f53b0da61c662cac51bb04e3cbfb2a8af9c71ac225760676f20db2f34c12fb674eac71ab995c3dbcfc7d9658e SHA512 4013676d6e79075fc0d31aa73effbdff8d391c122e5d168c93ed007c24f555a5f8c5e225461d074855b814e2c7d19ef1b804c3d82e5e5c018259e2907f2e168e AUX infernal-1.0.2-overflows.patch 540 BLAKE2B 1336442c3d1ef8a78d5d7a345bbbc3abf918d6edb0cef8fddcac32b9ece9f990464b3815592f564a05494a8b7c5c75e438349c384c29caa73c467e40f737db45 SHA512 c8bafb2c10d09cae24f882d5238b6ae974669d59e0ee583bcedb13e81c88ea9859c1f78343d5be91a5cca05a3dc07ffe6436b33e201a46baf349795da5eec906 -AUX infernal-1.0.2-parallel-build.patch 659 BLAKE2B ab11ef5e62268818d9cf4a871c82931ac85c564c3990fc06a4f74d8f826f4bda16150bde790681ac416ba40e0fc2cef9331942d30b25249a11a58434d56935e6 SHA512 d67271d858f60a5378d61892cd5c354ac95234620437621f3bf770e8829fa866a451ee031f530f502385044d7622f0fe88827614e95ab35ac6cbf8384d21e9c5 AUX infernal-1.0.2-perl-5.16-2.patch 4206 BLAKE2B eb4309d31e874f395d20bded4c132fb8b811fe17b4af5c95bd56ade05e22e7bf45c08e67884ca339aa7a2e13b2ddc9bb9527cbddef9458ce8fe05b7bd4707e49 SHA512 9784f31c18f6c53b15c0454d3a41db27c3f433ac3d3030bc113e9f9e8194fb51109de5055d038a3c639b1c4142d6fd0010825df484a857c9f072f43d8cadcb44 -AUX infernal-1.0.2-respect-DESTDIR.patch 396 BLAKE2B 822a6c543c0ad0a0ff75cc3fd50c4bbb84791cadcd4a93ad1a498b7464562dd00eea7424324f1bf715802c0dc9824dced0d16bd76d65ba9b7886b536b32fb988 SHA512 6847c87e45a34a68d179fbf8c9965af502cc9e52aa1f5ed800332dfb52e97ca3f2cb87a7dc4c3adb2d85f63567f15b084a50c7139f5ab03b0cf2b0711d023ec4 DIST infernal-1.0.2.tar.gz 15205421 BLAKE2B 3570ae42feb96ead383c2f1c09d34b4719ae0a5ae8fa973fd02f9ea6e8935c81ab49c7db21dad2e20c1ae6ab6fb9514f12704bbf5917f15f6582effae480312f SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af -EBUILD infernal-1.0.2-r1.ebuild 924 BLAKE2B 8a1af66f6ea82e8232d052d5361384a1082569344bf642b3e29b6f2d46dd1889c5780f3617e4d514857da013ec117e55cefa135aeb58587217746902da81b139 SHA512 816308be6a7e57e30f7c22e0c37662cde9b234501e324889e7e21e4d0e779cc6bb113490f10ce1aba3aeff46bdf9668442878e3cea4d5ad171beeb0e9fe6832c +EBUILD infernal-1.0.2-r1.ebuild 886 BLAKE2B 8f82a57ed31081abb50ee798ad80f3de5b7db8dbc3a3428b150de486834fae52253d9765d27a19276cbd79daf9a522c52733caf7a1ed824064932dbae3ade282 SHA512 af5e2dd5822150faa278e4160e41696a322deec3ac97e3df0cc100a1b8cebc929c747235a051ac86afed0269812f10dfb005160a56b49703aa67376064c49ad1 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch new file mode 100644 index 000000000000..41ab3103594b --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch @@ -0,0 +1,135 @@ +* Fix parallel build +* Respect AR +* Respect DESTDIR +* Respect LDFLAGS + +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -17,7 +17,6 @@ + # + CC = @CC@ + CFLAGS = @CFLAGS@ +-AR = @AR@ rcv + LN = ln + RANLIB = @RANLIB@ + LDFLAGS = -static @LDFLAGS@ +@@ -132,13 +131,13 @@ + esl_wuss.o + + all: libeasel.a +- (cd miniapps; make) ++ $(MAKE) -C miniapps + + .c.o: + ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< + + libeasel.a: $(OBJS) +- $(AR) libeasel.a $(OBJS) ++ $(AR) rcv libeasel.a $(OBJS) + $(RANLIB) libeasel.a + chmod 644 libeasel.a + +--- a/easel/testsuite/Makefile.in ++++ b/easel/testsuite/Makefile.in +@@ -15,7 +15,6 @@ + LIBS = @LIBGSL@ @LIBS@ -lm + MPILIBS = @MPILIBS@ + +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + ESLDIR = .. +--- a/iinfernal-1/Makefile.in ++++ b/iinfernal-1/Makefile.in +@@ -20,7 +20,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libhmmer.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + MPILIBS = @MPILIBS@ +@@ -63,7 +62,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + +--- a/Makefile.in ++++ b/Makefile.in +@@ -82,9 +82,10 @@ + all: core + + core: +- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) +- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) +- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ $(MAKE) -C easel ++ $(MAKE) -C src ++ $(MAKE) -C src module ++ $(MAKE) -C testsuite + + #.PHONY: $(RIGFILTERS) + #$(RIGFILTERS): core +@@ -202,9 +203,9 @@ + # "make install" installs the programs in BINDIR + # + install: +- mkdir -p ${BINDIR} ++ mkdir -p $(DESTDIR)${BINDIR} + for file in $(PROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ + done + # if test -d $(RIGFILTERS); then\ + # for file in $(RFPROGS); do\ +--- a/rigfilters/cfsqp/Makefile.in ++++ b/rigfilters/cfsqp/Makefile.in +@@ -24,7 +24,6 @@ + ## archiving command, and ranlib command. + # these are used to create the libcfsqp.a library, necessary for cm2hmm + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + OBJS = cfsqp.o\ +@@ -41,7 +40,7 @@ + all: libcfsqp.a + + libcfsqp.a: $(OBJS) ${HDRS} +- $(AR) libcfsqp.a $(OBJS) ++ $(AR) rcv libcfsqp.a $(OBJS) + $(RANLIB) libcfsqp.a + chmod 644 libcfsqp.a + +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -27,7 +27,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libinfernal.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + # configuration for optional MPI functionality +@@ -86,7 +85,7 @@ + all: $(PROGS) + + $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} +- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) + + + ################################################################# +@@ -95,7 +94,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) ${HDRS} +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch deleted file mode 100644 index f688dce152ed..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch +++ /dev/null @@ -1,15 +0,0 @@ -Respect LDFLAGS - -http://bugs.gentoo.org/show_bug.cgi?id=338177 - ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -86,7 +86,7 @@ - all: $(PROGS) - - $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} -- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) -+ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) - - - ################################################################# diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch deleted file mode 100644 index 67ffa6fda7f6..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch +++ /dev/null @@ -1,31 +0,0 @@ -Fix parallel build - -http://bugs.gentoo.org/show_bug.cgi?id=311919 - ---- a/Makefile.in -+++ b/Makefile.in -@@ -82,9 +82,10 @@ - all: core - - core: -- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) -- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) -- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") -+ $(MAKE) -C easel -+ $(MAKE) -C src -+ $(MAKE) -C src module -+ $(MAKE) -C testsuite - - #.PHONY: $(RIGFILTERS) - #$(RIGFILTERS): core ---- a/easel/Makefile.in -+++ b/easel/Makefile.in -@@ -132,7 +132,7 @@ - esl_wuss.o - - all: libeasel.a -- (cd miniapps; make) -+ $(MAKE) -C miniapps - - .c.o: - ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch deleted file mode 100644 index ea465e592ffa..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch +++ /dev/null @@ -1,16 +0,0 @@ -Build system does not respect DESTDIR by default. - ---- a/Makefile.in -+++ b/Makefile.in -@@ -203,9 +203,9 @@ - # "make install" installs the programs in BINDIR - # - install: -- mkdir -p ${BINDIR} -+ mkdir -p $(DESTDIR)${BINDIR} - for file in $(PROGS); do\ -- cp src/$$file $(BINDIR)/;\ -+ cp src/$$file $(DESTDIR)$(BINDIR)/;\ - done - # if test -d $(RIGFILTERS); then\ - # for file in $(RFPROGS); do\ diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild index e906c23024ff..2e96418b6bb9 100644 --- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 + +inherit toolchain-funcs DESCRIPTION="Inference of RNA alignments" HOMEPAGE="http://infernal.janelia.org/" @@ -9,21 +11,20 @@ SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -IUSE="mpi" KEYWORDS="amd64 x86" +IUSE="mpi" RDEPEND="mpi? ( virtual/mpi )" DEPEND="${RDEPEND}" PATCHES=( - "${FILESDIR}"/${P}-parallel-build.patch + "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-overflows.patch "${FILESDIR}"/${P}-perl-5.16-2.patch - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-respect-DESTDIR.patch ) src_configure() { + tc-export AR econf $(use_enable mpi) } -- cgit v1.2.3