sci-biology/phred: Revbump to EAPI=6

Package-Manager: portage-2.3.1

5 files changed, 170 insertions, 41 deletions

diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
index 92cfe6ce81b8..c326374708c9 100644
--- a/sci-biology/phred/Manifest
+++ b/sci-biology/phred/Manifest
@@ -1 +1 @@
-DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975
+DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975 SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 WHIRLPOOL 9b14cfb1ca970a14ef613ca17efb82955c0ecec414dfad8835c883650f306b3a79846b7a410a9359cbd9ca953d890673366b6f865a2a357e81213d34b3327d3e
diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch
new file mode 100644
index 000000000000..997f39941a07
--- /dev/null
+++ b/sci-biology/phred/files/phred-071220-fix-build-system.patch
@@ -0,0 +1,82 @@
+* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS
+* Specify a default target, in order to keep the ebuild slim
+
+--- a/Makefile
++++ b/Makefile
+@@ -12,9 +12,9 @@
+ 
+ # UNIX specific definitions (default)
+ #
+-CC= cc
+-CFLAGS= -O -DANSI_C $(LXFLAGS)
+-CLIB= -lm
++CC ?= cc
++CPPFLAGS += -DANSI_C $(LXFLAGS)
++LIBS += -lm
+ 
+ # Windows 'nmake' specific definitions
+ #
+@@ -133,9 +133,6 @@
+   $(objdir)writeSDF.o \
+   $(objdir)writeSeq.o
+ 
+-SRCS = $(OBJS:.o=.c)
+-WOBJ = $(OBJS:.o=.obj)
+-
+ INCS = \
+   $(incdir)chromatData.h \
+   $(incdir)freeChromatData.h \
+@@ -179,48 +176,18 @@
+ # UNIX make specific phred target
+ # note: a horizontal tab character must precede `$(CC)'
+ #
+-phred: $(OBJS)
+-	$(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB)
+ 
+ 
+-# Windows nmake specific phred target
+-#
+-forwindows: $(WOBJ)
+-	$(CC) $(CFLAGS) /Fephred $(WOBJ)
+-#	$(CC) $(CFLAGS) /Fedaev daev.c
++.PHONY: all
++all: phred daev
+ 
+ 
+-# test CC: refuse to compile if
+-#
+-#   o  SunOS
+-#
+-#   AND
+-#
+-#   o  using /usr/ucb/cc compiler
+-#
+-#   NOTE: this compiler causes problems: see PHRED.DOC
+-#
+-test_cc:
+-	@if [ `uname` = SunOS ] ; \
+-        then \
+-          if [ `which $(CC)` = "/usr/ucb/cc" ] ; \
+-          then \
+-            echo ""; \
+- echo "============================================================"; \
+- echo "|                                                          |"; \
+- echo "|   This SUN C compiler produces a bad phred executable.   |"; \
+- echo "|                                                          |"; \
+- echo "|   Please see the PHRED.DOC file for more information.    |"; \
+- echo "|                                                          |"; \
+- echo "============================================================"; \
+-            echo ""; \
+-             exit 1; \
+-          fi \
+-        fi
++phred: $(OBJS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS)
+ 
+ 
+ daev: daev.o
+-	$(CC) $(CFLAGS) -o daev daev.o -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS)
+ 
+ 
+ clean:
diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch
new file mode 100644
index 000000000000..ab4d2ea023f6
--- /dev/null
+++ b/sci-biology/phred/files/phred-071220-fix-qa.patch
@@ -0,0 +1,36 @@
+Fix implicit declarations:
+* daev.c: In function ‘processParameters’:
+* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration]
+*          if( !isdigit( argv[iarg][0] ) )
+
+--- a/autoPhred.c
++++ b/autoPhred.c
+@@ -57,6 +57,7 @@
+ static int xstrcmp();
+ #endif
+ 
++int freeMBRData( MBRData *mbrData );
+ #ifdef ANSI_C
+ int autoPhred( Option *option )
+ #else
+--- a/daev.c
++++ b/daev.c
+@@ -58,6 +58,7 @@
+ #include <sys/stat.h>
+ #include <time.h>
+ #include <math.h>
++#include <ctype.h>
+ 
+ #ifndef _WIN32
+ #include <dirent.h>
+--- a/mergedBaseRead.c
++++ b/mergedBaseRead.c
+@@ -63,7 +63,7 @@
+   Peak *peak;
+   Observed_peak *obs_peak;
+ 
+-  static initFlag = 0;
++  static int initFlag = 0;
+   static char mchar[256][256];
+ 
+   if( initFlag == 0 )
diff --git a/sci-biology/phred/phred-071220-r1.ebuild b/sci-biology/phred/phred-071220-r1.ebuild
new file mode 100644
index 000000000000..acaf74e7d430
--- /dev/null
+++ b/sci-biology/phred/phred-071220-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="A base caller for Sanger DNA sequencing"
+HOMEPAGE="http://phrap.org/phredphrapconsed.html"
+SRC_URI="phred-dist-071220.b-acd.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+PATCHES=(
+	"${FILESDIR}/${PN}-071220-fix-build-system.patch"
+	"${FILESDIR}/${PN}-071220-fix-qa.patch"
+)
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "${SRC_URI}, then place it in ${DISTDIR}"
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dobin phred daev
+
+	insinto /usr/share/${PN}
+	doins phredpar.dat
+
+	echo "PHRED_PARAMETER_FILE=${EPREFIX}/usr/share/${PN}/phredpar.dat" > 99phred || die
+	doenvd 99phred
+
+	newdoc DAEV.DOC DAEV.DOC.txt
+	newdoc PHRED.DOC PHRED.DOC.txt
+}
diff --git a/sci-biology/phred/phred-071220.ebuild b/sci-biology/phred/phred-071220.ebuild
deleted file mode 100644
index 22600ba92c50..000000000000
--- a/sci-biology/phred/phred-071220.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-DESCRIPTION="A base caller for Sanger DNA sequencing"
-HOMEPAGE="http://phrap.org/phredphrapconsed.html"
-SRC_URI="phred-dist-071220.b-acd.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	elog "Please visit ${HOMEPAGE} and obtain the file"
-	elog "${SRC_URI}, then place it in ${DISTDIR}"
-}
-
-src_compile() {
-	sed -i -e 's/CFLAGS=/CFLAGS += /' Makefile
-	emake daev || die
-	emake || die
-}
-
-src_install() {
-	dobin phred daev || die
-	insinto /usr/share/${PN}
-	doins phredpar.dat || die
-	echo "PHRED_PARAMETER_FILE=/usr/share/${PN}/phredpar.dat" > 99phred
-	doenvd 99phred || die
-	newdoc DAEV.DOC DAEV.DOC.txt
-	newdoc PHRED.DOC PHRED.DOC.txt
-}