sci-biology/infernal: [QA] Pass AR to build system

Closes: https://bugs.gentoo.org/725320
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: David Seifert <soap@gentoo.org>

5 files changed, 142 insertions, 68 deletions

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)
 }