sci-chemistry/aqua: QA fixes and EAPI bump

* Bump to EAPI 6
* Respect CFLAGS
* Add missing build dep
* Generate missing checksums

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=614230
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec@gentoo.org>

3 files changed, 24 insertions, 21 deletions

diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest
index 187beb2cef9c..84673718e67e 100644
--- a/sci-chemistry/aqua/Manifest
+++ b/sci-chemistry/aqua/Manifest
@@ -1,2 +1,2 @@
-DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996
+DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996 SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f WHIRLPOOL 181d320edd32faaac71a48163975ab6899221d7c85744eedfb8954d3360c974a0c8223b8b0f00375e2369fa7350df2e16a1062698be01c625ef00308a8ee0887
 DIST aqua3.2.tar.gz 688408 SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a WHIRLPOOL 458fc0e574273fd9d2647ef8b2788c98669c9f96133f7132eddc9cbfb981e42894f5e4fd0e8d67f52ddb4c6424399b21973d4d87a175b440d81b7b955fe3fe41
diff --git a/sci-chemistry/aqua/aqua-3.2-r2.ebuild b/sci-chemistry/aqua/aqua-3.2-r3.ebuild
index 335e68850404..74e4e60416f7 100644
--- a/sci-chemistry/aqua/aqua-3.2-r2.ebuild
+++ b/sci-chemistry/aqua/aqua-3.2-r3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=6
 
-inherit eutils fortran-2 toolchain-funcs
+inherit fortran-2 toolchain-funcs
 
 DESCRIPTION="Program suite in this distribution calculates restraint violations"
 HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
@@ -17,12 +17,16 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc examples"
 
 RDEPEND="sci-chemistry/procheck"
-DEPEND=""
+DEPEND="app-shells/tcsh"
 
 RESTRICT="fetch"
 
 S="${WORKDIR}"/${PN}${PV}
 
+PATCHES=(
+	"${FILESDIR}"/${P}-flags.patch
+)
+
 pkg_nofetch() {
 	elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
 	elog "And follow the instruction for downloading ${PN}${PV}.tar.gz ->  ${DISTDIR}/${PN}${PV}.tar.gz."
@@ -37,11 +41,11 @@ src_prepare() {
 		-e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \
 		-e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \
 		-i $(find . -type f) || die
-	epatch "${FILESDIR}"/${PV}-flags.patch
+	default
 }
 
 src_compile() {
-	pushd src > /dev/null
+	cd src || die
 	emake \
 		MYROOT="${WORKDIR}" \
 		CC="$(tc-getCC)" \
@@ -57,7 +61,6 @@ src_compile() {
 		CFLAGS="${CFLAGS} -I../sub/lib" \
 		FFLAGS="${FFLAGS}" \
 		LDFLAGS="${LDFLAGS}"
-	popd
 }
 
 src_install() {
diff --git a/sci-chemistry/aqua/files/3.2-flags.patch b/sci-chemistry/aqua/files/aqua-3.2-flags.patch
index cd12fbb9a324..a60841b8ce08 100644
--- a/sci-chemistry/aqua/files/3.2-flags.patch
+++ b/sci-chemistry/aqua/files/aqua-3.2-flags.patch
@@ -7,39 +7,39 @@ index 3113471..dd7a320 100644
  
  $(BIN)/AquaWhat:    AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
 -	$(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS)
  
  $(BIN)/AquaHow:	    AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
 -	$(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS)
  
  $(BIN)/AquaPseudo:  AquaPseudo.o $(OBJECTS) $(R_OBJECTS) 
 -	$(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS)
  
  $(BIN)/AquaDist:    AquaDist.o $(OBJECTS) 
 -	$(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm
  
  $(BIN)/AquaCalc:    AquaCalc.o $(OBJECTS) $(RNG_OBJECTS)
 -	$(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm
  
  $(BIN)/AquaAssign:  AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
 -	$(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
  
  $(BIN)/AquaCompl:  AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) 
 -	$(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm  
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm  
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm
  
  $(BIN)/AquaRedun:  AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) 
 -	$(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS)
  
  $(BIN)/testnew:	    testnew.o $(OBJECTS)
 -	$(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS)
  
  $(BIN)/getproj:    getproj.c 
 -	$(CC) -o $(BIN)/getproj -O getproj.c
@@ -47,20 +47,20 @@ index 3113471..dd7a320 100644
  
  $(BIN)/AquaPlot:    AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
 -	$(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
  
  $(BIN)/Qext:	   Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
 -	$(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o
  
  $(BIN)/StarTest:	StarTest.o
 -	$(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS)
-+	$(CC) $(LDFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS)
  
  exth:		exth.f
 -	f77 -o exth -O2 exth.f
 -	strip exth
-+	$(FC) $(FFLAGS) -o exth -O2 exth.f
++	$(FC) $(FFLAGS) $(LDFLAGS) -o exth -O2 exth.f
  
  
  # Object files