[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/, sci-biology/bedops/files/
commit: 80338ed685ac288857f35b4eb678f1a3bf026783
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Mar 16 18:18:58 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Mar 16 18:18:58 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=80338ed6
Revert "sci-biology/bedops: drop old"
This reverts commit 96b52ed1a41aa7598caeb8fef408a50dfd57715b.
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/bedops/bedops-2.4.26.ebuild| 31 +
.../files/bedops-2.4.26-respect-cxxflags.patch | 138 +
2 files changed, 169 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 0..4ae167a08
--- /dev/null
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -0,0 +1,31 @@
+# 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 ${PATCHES[@]}
+}
+
+src_install(){
+ emake install
+ dobin bin/*
+ dodoc README.md
+}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
new file mode 100644
index 0..16ac4e2b0
--- /dev/null
+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
@@ -0,0 +1,138 @@
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori
2017-03-14 08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin
2017-04-28 21:53:55.811777276 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${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} ${INCLUDES}
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14
08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28
21:54:05.952048644 +0200
+@@ -24,7 +24,7 @@
+ INCLUDES= -iquote$(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 $(BINDIR)
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori
2017-03-14 08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28
21:54:12.162214836 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${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} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14
08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28
21:54:19.472410465 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES= -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
+ LIBRARI
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/
commit: ed8933c21d757ecbedbe330621af864ab0cbf6b2
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Mar 16 18:22:13 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Mar 16 18:22:13 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed8933c2
sci-biology/bedops: fixup the old version
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/bedops/bedops-2.4.26.ebuild | 16
1 file changed, 4 insertions(+), 12 deletions(-)
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild
b/sci-biology/bedops/bedops-2.4.26.ebuild
index 4ae167a08..0bdabc617 100644
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit toolchain-funcs eutils
+inherit toolchain-funcs
DESCRIPTION="Manipulate BED file (alternative to bedtools)"
HOMEPAGE="http://bedops.readthedocs.io
@@ -13,16 +13,8 @@
SRC_URI="https://github.com/bedops/bedops/archive/v${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 ${PATCHES[@]}
-}
+PATCHES=( "${FILESDIR}"/${P}-respect-cxxflags.patch )
src_install(){
emake install
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/files/, sci-biology/bedops/
commit: 96b52ed1a41aa7598caeb8fef408a50dfd57715b
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 09:36:21 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 09:36:21 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=96b52ed1
sci-biology/bedops: drop old
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/bedops/bedops-2.4.26.ebuild| 31 -
.../files/bedops-2.4.26-respect-cxxflags.patch | 138 -
2 files changed, 169 deletions(-)
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild
b/sci-biology/bedops/bedops-2.4.26.ebuild
deleted file mode 100644
index 4ae167a08..0
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs eutils
-
-DESCRIPTION="Manipulate BED file (alternative to bedtools)"
-HOMEPAGE="http://bedops.readthedocs.io
- https://github.com/bedops/bedops";
-SRC_URI="https://github.com/bedops/bedops/archive/v${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 ${PATCHES[@]}
-}
-
-src_install(){
- emake install
- dobin bin/*
- dodoc README.md
-}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
deleted file mode 100644
index 16ac4e2b0..0
--- a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
+++ /dev/null
@@ -1,138 +0,0 @@
bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori
2017-03-14 08:43:22.0 +0100
-+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin
2017-04-28 21:53:55.811777276 +0200
-@@ -28,7 +28,7 @@
- LIBLOCATION = -L${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} ${INCLUDES}
bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14
08:43:22.0 +0100
-+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28
21:54:05.952048644 +0200
-@@ -24,7 +24,7 @@
- INCLUDES= -iquote$(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 $(BINDIR)
bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori
2017-03-14 08:43:22.0 +0100
-+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28
21:54:12.162214836 +0200
-@@ -28,7 +28,7 @@
- LIBLOCATION = -L${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} ${INCLUDES}
-
bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14
08:43:22.0 +0100
-+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28
21:54:19.472410465 +0200
-@@ -23,7 +23,7 @@
- INCLUDES= -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
- LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
- LIBRARIES = ${L
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/
commit: 9ee2acd37be1d4f134e871e0c596d916d7d4368a
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 09:36:00 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 09:36:00 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ee2acd3
sci-biology/bedops: version bump EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/bedops/bedops-2.4.39.ebuild | 24
1 file changed, 24 insertions(+)
diff --git a/sci-biology/bedops/bedops-2.4.39.ebuild
b/sci-biology/bedops/bedops-2.4.39.ebuild
new file mode 100644
index 0..3f8f956bb
--- /dev/null
+++ b/sci-biology/bedops/bedops-2.4.39.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Manipulate BED file (alternative to bedtools)"
+HOMEPAGE="http://bedops.readthedocs.io
+ https://github.com/bedops/bedops";
+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+ emake install
+ dobin bin/*
+ dodoc README.md
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/
commit: 2a28ea64417794f6c09e39345fec05445ff8ae44
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Dec 18 10:53:44 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Dec 18 10:54:07 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a28ea64
sci-biology/bedops: fix install procedure
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/bedops/bedops-2.4.26.ebuild | 8 +++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild
b/sci-biology/bedops/bedops-2.4.26.ebuild
index d281fbede..4ae167a08 100644
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -23,3 +23,9 @@ src_prepare(){
local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
epatch ${PATCHES[@]}
}
+
+src_install(){
+ emake install
+ dobin bin/*
+ dodoc README.md
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/
commit: 1ef384168f532e750c2c925cde2487d1b27fb459 Author: Justin Lecher gentoo org> AuthorDate: Sat Apr 29 18:22:00 2017 + Commit: Justin Lecher gentoo org> CommitDate: Sat Apr 29 18:22:00 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ef38416 Add new remote ID Signed-off-by: Justin Lecher gentoo.org> sci-biology/bedops/metadata.xml | 5 - 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml index f68a1b6fa..275007996 100644 --- a/sci-biology/bedops/metadata.xml +++ b/sci-biology/bedops/metadata.xml @@ -1,4 +1,4 @@ - + http://www.gentoo.org/dtd/metadata.dtd";> @@ -9,4 +9,7 @@ sci-biol...@gentoo.org Gentoo Biology Project + +bedops/bedops +
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/files/, sci-biology/bedops/
commit: 738b58d5c8eead005941421868ac2787b7ce570d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Apr 28 20:11:15 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Apr 28 20:11:15 2017 +
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 0..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 ${PATCHES[@]}
+}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
new file mode 100644
index 0..16ac4e2b0
--- /dev/null
+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
@@ -0,0 +1,138 @@
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori
2017-03-14 08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin
2017-04-28 21:53:55.811777276 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${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} ${INCLUDES}
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14
08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28
21:54:05.952048644 +0200
+@@ -24,7 +24,7 @@
+ INCLUDES= -iquote$(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 $(BINDIR)
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori
2017-03-14 08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28
21:54:12.162214836 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${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} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14
08:43:22.0 +0100
bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28
21:54:19.472410465 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES= -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR}
-I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDI
