commit: 6e813f13ba23ea1b7adc4b635b4d9508d0a9954c Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Oct 2 22:20:26 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Oct 3 20:21:00 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6e813f13
sci-biology/phred: Revbump to EAPI=6 Package-Manager: portage-2.3.1 sci-biology/phred/Manifest | 2 +- .../files/phred-071220-fix-build-system.patch | 82 ++++++++++++++++++++++ sci-biology/phred/files/phred-071220-fix-qa.patch | 36 ++++++++++ sci-biology/phred/phred-071220-r1.ebuild | 51 ++++++++++++++ sci-biology/phred/phred-071220.ebuild | 40 ----------- 5 files changed, 170 insertions(+), 41 deletions(-) diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest index 92cfe6c..c326374 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 00000000..997f399 --- /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 00000000..ab4d2ea --- /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 00000000..acaf74e --- /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 22600ba..00000000 --- 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 -}
