gentoo resync : 29.06.2020

6 files changed, 144 insertions, 72 deletions

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)
 }