* [gentoo-commits] proj/sci:master commit in: sci-biology/bedops/files/, sci-biology/bedops/
@ 2017-04-28 20:11 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2017-04-28 20:11 UTC (permalink / raw
To: gentoo-commits
commit: 738b58d5c8eead005941421868ac2787b7ce570d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 28 20:11:15 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 28 20:11:15 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=738b58d5
sci-biology/bedops: new package
The patch does not expand properly CXXFLAGS for some reason.
The package conatains bundled zlib. bzip2 and other 3rd-party stuff.
It compile statically at least some binaries.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/bedops/bedops-2.4.26.ebuild | 25 ++++
.../files/bedops-2.4.26-respect-cxxflags.patch | 138 +++++++++++++++++++++
sci-biology/bedops/metadata.xml | 12 ++
3 files changed, 175 insertions(+)
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
new file mode 100644
index 000000000..d281fbede
--- /dev/null
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs eutils
+
+DESCRIPTION="Manipulate BED file (alternative to bedtools)"
+HOMEPAGE="http://bedops.readthedocs.io
+ https://github.com/bedops/bedops"
+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ default
+ local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
+ epatch ${PATCHES[@]}
+}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
new file mode 100644
index 000000000..16ac4e2b0
--- /dev/null
+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
@@ -0,0 +1,138 @@
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200
+@@ -24,7 +24,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+@@ -64,4 +64,4 @@
+ rm -rf $(OBJDIR)
+ rm -f $(BINDIR)/$(PROG)
+ rm -f $(BINDIR)/*.$(PROG)
+- rm -rf $(BINDIR)
+\ No newline at end of file
++ rm -rf $(BINDIR)
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200
+@@ -1,7 +1,7 @@
+ MIN_OSX_VERSION = 10.7
+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS = -O3
++CFLAGS = ${CXXFLAGS:--O3}
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200
+@@ -1,6 +1,6 @@
+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS = -O3
++CFLAGS = ${CXXFLAGS:--O3}
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200
+@@ -27,7 +27,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200
+@@ -25,7 +25,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200
+@@ -7,7 +7,7 @@
+ PROG = sort-bed
+ DIST_DIR = ../bin
+ OBJ_DIR = objects_${ARCH}
+-OPTIMIZE = -O3 -std=c++11 -stdlib=libc++
++OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
+ WARNINGS = -Wall
+ MAIN = ../../../..
+ HEAD = ${MAIN}/interfaces/general-headers
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200
+@@ -29,7 +29,7 @@
+ BINDIR = ../bin
+ OBJDIR = objects
+ WARNINGS = -Wall -Wextra -pedantic
+-BLDFLAGS = ${WARNINGS} -O3 -std=c++11
++BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/bedops/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bedops/files/, sci-biology/bedops/
@ 2021-03-06 10:02 Andrew Ammerlaan
0 siblings, 0 replies; 2+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 10:02 UTC (permalink / raw
To: gentoo-commits
commit: 96b52ed1a41aa7598caeb8fef408a50dfd57715b
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 09:36:21 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 09:36:21 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=96b52ed1
sci-biology/bedops: drop old
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/bedops/bedops-2.4.26.ebuild | 31 -----
.../files/bedops-2.4.26-respect-cxxflags.patch | 138 ---------------------
2 files changed, 169 deletions(-)
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
deleted file mode 100644
index 4ae167a08..000000000
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs eutils
-
-DESCRIPTION="Manipulate BED file (alternative to bedtools)"
-HOMEPAGE="http://bedops.readthedocs.io
- https://github.com/bedops/bedops"
-SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare(){
- default
- local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
- epatch ${PATCHES[@]}
-}
-
-src_install(){
- emake install
- dobin bin/*
- dodoc README.md
-}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
deleted file mode 100644
index 16ac4e2b0..000000000
--- a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
+++ /dev/null
@@ -1,138 +0,0 @@
---- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200
-@@ -28,7 +28,7 @@
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
- STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
--BLDFLAGS = -O3 ${STDFLAGS}
-+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
-
-
- FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
---- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200
-@@ -24,7 +24,7 @@
- INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
--BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
- SFLAGS = -static
-
- dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
-@@ -64,4 +64,4 @@
- rm -rf $(OBJDIR)
- rm -f $(BINDIR)/$(PROG)
- rm -f $(BINDIR)/*.$(PROG)
-- rm -rf $(BINDIR)
-\ No newline at end of file
-+ rm -rf $(BINDIR)
---- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200
-@@ -28,7 +28,7 @@
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
- STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
--BLDFLAGS = -O3 ${STDFLAGS}
-+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
-
- FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
-
---- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200
-@@ -23,7 +23,7 @@
- INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
--BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
- SFLAGS = -static
-
- dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
---- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200
-@@ -1,7 +1,7 @@
- MIN_OSX_VERSION = 10.7
- BLDFLAGS = -Wall -Wextra -pedantic -std=c99
- COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
--CFLAGS = -O3
-+CFLAGS = ${CXXFLAGS:--O3}
- CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
- CPFLAGS = -pg
- LIBS = -lpthread
---- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200
-@@ -1,6 +1,6 @@
- BLDFLAGS = -Wall -Wextra -pedantic -std=c99
- COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
--CFLAGS = -O3
-+CFLAGS = ${CXXFLAGS:--O3}
- CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
- CPFLAGS = -pg
- LIBS = -lpthread
---- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200
-@@ -27,7 +27,7 @@
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
- STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
--BLDFLAGS = -O3 ${STDFLAGS}
-+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
-
- FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
-
---- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200
-@@ -25,7 +25,7 @@
- INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
--BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
- SFLAGS = -static
-
- dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
---- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200
-@@ -28,7 +28,7 @@
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
- STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
--BLDFLAGS = -O3 ${STDFLAGS}
-+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
-
- FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
-
---- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200
-@@ -23,7 +23,7 @@
- INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
- LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
--BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
- SFLAGS = -static
-
- dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
---- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200
-@@ -7,7 +7,7 @@
- PROG = sort-bed
- DIST_DIR = ../bin
- OBJ_DIR = objects_${ARCH}
--OPTIMIZE = -O3 -std=c++11 -stdlib=libc++
-+OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
- WARNINGS = -Wall
- MAIN = ../../../..
- HEAD = ${MAIN}/interfaces/general-headers
---- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
-+++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200
-@@ -29,7 +29,7 @@
- BINDIR = ../bin
- OBJDIR = objects
- WARNINGS = -Wall -Wextra -pedantic
--BLDFLAGS = ${WARNINGS} -O3 -std=c++11
-+BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
- SFLAGS = -static
-
- dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
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2017-04-28 20:11 Martin Mokrejs
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