[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/files/, sci-biology/bedops/ - gentoo-commits

From:	Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To:	gentoo-commits@l.g.o
Subject:	[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/files/, sci-biology/bedops/
Date:	Fri, 28 Apr 2017 20:11:33
Message-Id:	`1493410275.738b58d5c8eead005941421868ac2787b7ce570d.mmokrejs@gentoo`

1

commit:     738b58d5c8eead005941421868ac2787b7ce570d

2

Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>

3

AuthorDate: Fri Apr 28 20:11:15 2017 +0000

4

Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>

5

CommitDate: Fri Apr 28 20:11:15 2017 +0000

6

URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=738b58d5

7

8

sci-biology/bedops: new package

9

10

The patch does not expand properly CXXFLAGS for some reason.

11

The package conatains bundled zlib. bzip2 and other 3rd-party stuff.

12

It compile statically at least some binaries.

13

14

Package-Manager: Portage-2.3.5, Repoman-2.3.2

15

16

 sci-biology/bedops/bedops-2.4.26.ebuild            |  25 ++++

17

 .../files/bedops-2.4.26-respect-cxxflags.patch     | 138 +++++++++++++++++++++

18

 sci-biology/bedops/metadata.xml                    |  12 ++

19

 3 files changed, 175 insertions(+)

20

21

diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild

22

new file mode 100644

23

index 000000000..d281fbede

24

--- /dev/null

25

+++ b/sci-biology/bedops/bedops-2.4.26.ebuild

26

@@ -0,0 +1,25 @@

27

+# Copyright 1999-2017 Gentoo Foundation

28

+# Distributed under the terms of the GNU General Public License v2

29

+

30

+EAPI=6

31

+

32

+inherit toolchain-funcs eutils

33

+

34

+DESCRIPTION="Manipulate BED file (alternative to bedtools)"

35

+HOMEPAGE="http://bedops.readthedocs.io

36

+	https://github.com/bedops/bedops"

37

+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"

38

+

39

+LICENSE="GPL-2"

40

+SLOT="0"

41

+KEYWORDS="~amd64 ~x86"

42

+IUSE=""

43

+

44

+DEPEND=""

45

+RDEPEND="${DEPEND}"

46

+

47

+src_prepare(){

48

+	default

49

+	local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)

50

+	epatch ${PATCHES[@]}

51

+}

52

53

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

54

new file mode 100644

55

index 000000000..16ac4e2b0

56

--- /dev/null

57

+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch

58

@@ -0,0 +1,138 @@

59

+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100

60

++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin	2017-04-28 21:53:55.811777276 +0200

61

+@@ -28,7 +28,7 @@

62

+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}

63

+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

64

+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++

65

+-BLDFLAGS             = -O3 ${STDFLAGS}

66

++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}

67

+

68

+

69

+ 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}

70

+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100

71

++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile	2017-04-28 21:54:05.952048644 +0200

72

+@@ -24,7 +24,7 @@

73

+ INCLUDES                = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}

74

+ LIBLOCATION             = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}

75

+ LIBRARIES               = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

76

+-BLDFLAGS                = -Wall -pedantic -O3 -std=c++11

77

++BLDFLAGS                = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11

78

+ SFLAGS                  = -static

79

+

80

+ dependency_names        = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding

81

+@@ -64,4 +64,4 @@

82

+ 	rm -rf $(OBJDIR)

83

+ 	rm -f $(BINDIR)/$(PROG)

84

+ 	rm -f $(BINDIR)/*.$(PROG)

85

+-	rm -rf $(BINDIR)

86

+\ No newline at end of file

87

++	rm -rf $(BINDIR)

88

+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100

89

++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin	2017-04-28 21:54:12.162214836 +0200

90

+@@ -28,7 +28,7 @@

91

+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}

92

+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

93

+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++

94

+-BLDFLAGS             = -O3 ${STDFLAGS}

95

++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}

96

+

97

+ 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}

98

+

99

+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100

100

++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile	2017-04-28 21:54:19.472410465 +0200

101

+@@ -23,7 +23,7 @@

102

+ INCLUDES            = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}

103

+ LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}

104

+ LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

105

+-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11 

106

++BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 

107

+ SFLAGS              = -static

108

+

109

+ dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding

110

+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100

111

++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin	2017-04-28 21:54:25.422569698 +0200

112

+@@ -1,7 +1,7 @@

113

+ MIN_OSX_VERSION           = 10.7

114

+ BLDFLAGS                  = -Wall -Wextra -pedantic -std=c99

115

+ COMMONFLAGS               = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1

116

+-CFLAGS                    = -O3

117

++CFLAGS                    = ${CXXFLAGS:--O3}

118

+ CDFLAGS                   = -DDEBUG=1 -g -O0 -fno-inline

119

+ CPFLAGS                   = -pg

120

+ LIBS                      = -lpthread

121

+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100

122

++++ bedops-2.4.26/applications/bed/conversion/src/Makefile	2017-04-28 21:54:30.832714482 +0200

123

+@@ -1,6 +1,6 @@

124

+ BLDFLAGS                  = -Wall -Wextra -pedantic -std=c99

125

+ COMMONFLAGS               = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1

126

+-CFLAGS                    = -O3

127

++CFLAGS                    = ${CXXFLAGS:--O3}

128

+ CDFLAGS                   = -DDEBUG=1 -g -O0 -fno-inline

129

+ CPFLAGS                   = -pg

130

+ LIBS                      = -lpthread

131

+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100

132

++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin	2017-04-28 21:54:37.312887898 +0200

133

+@@ -27,7 +27,7 @@

134

+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}

135

+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

136

+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++

137

+-BLDFLAGS             = -O3 ${STDFLAGS}

138

++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}

139

+

140

+ 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}

141

+

142

+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100

143

++++ bedops-2.4.26/applications/bed/bedops/src/Makefile	2017-04-28 21:54:43.513053823 +0200

144

+@@ -25,7 +25,7 @@

145

+ INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}

146

+ LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}

147

+ LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

148

+-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11

149

++BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11

150

+ SFLAGS              = -static

151

+

152

+ dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding

153

+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100

154

++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin	2017-04-28 21:54:49.093203153 +0200

155

+@@ -28,7 +28,7 @@

156

+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}

157

+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

158

+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++

159

+-BLDFLAGS             = -O3 ${STDFLAGS}

160

++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}

161

+

162

+ 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}

163

+

164

+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100

165

++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile	2017-04-28 21:54:54.283342049 +0200

166

+@@ -23,7 +23,7 @@

167

+ INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}

168

+ LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}

169

+ LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}

170

+-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11

171

++BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11

172

+ SFLAGS              = -static

173

+

174

+ dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding

175

+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100

176

++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin	2017-04-28 21:55:00.023495662 +0200

177

+@@ -7,7 +7,7 @@

178

+ PROG                 = sort-bed

179

+ DIST_DIR             = ../bin

180

+ OBJ_DIR              = objects_${ARCH}

181

+-OPTIMIZE             = -O3 -std=c++11 -stdlib=libc++

182

++OPTIMIZE             = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++

183

+ WARNINGS             = -Wall

184

+ MAIN                 = ../../../..

185

+ HEAD                 = ${MAIN}/interfaces/general-headers

186

+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100

187

++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile	2017-04-28 21:55:05.663646597 +0200

188

+@@ -29,7 +29,7 @@

189

+ BINDIR              = ../bin

190

+ OBJDIR             = objects

191

+ WARNINGS            = -Wall -Wextra -pedantic

192

+-BLDFLAGS            = ${WARNINGS} -O3 -std=c++11

193

++BLDFLAGS            = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11

194

+ SFLAGS              = -static

195

+

196

+ dependency_names    = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort

197

198

diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml

199

new file mode 100644

200

index 000000000..f68a1b6fa

201

--- /dev/null

202

+++ b/sci-biology/bedops/metadata.xml

203

@@ -0,0 +1,12 @@

204

+<?xml version="1.0" encoding="UTF-8"?>

205

+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">

206

+<pkgmetadata>

207

+  <maintainer type="person">

208

+    <email>mmokrejs@×××××××××××××××.cz</email>

209

+    <name>Martin Mokrejs</name>

210

+  </maintainer>

211

+  <maintainer type="project">

212

+    <email>sci-biology@g.o</email>

213

+    <name>Gentoo Biology Project</name>

214

+  </maintainer>

215

+</pkgmetadata>

1	commit: 738b58d5c8eead005941421868ac2787b7ce570d
2	Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3	AuthorDate: Fri Apr 28 20:11:15 2017 +0000
4	Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5	CommitDate: Fri Apr 28 20:11:15 2017 +0000
6	URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=738b58d5
7
8	sci-biology/bedops: new package
9
10	The patch does not expand properly CXXFLAGS for some reason.
11	The package conatains bundled zlib. bzip2 and other 3rd-party stuff.
12	It compile statically at least some binaries.
13
14	Package-Manager: Portage-2.3.5, Repoman-2.3.2
15
16	sci-biology/bedops/bedops-2.4.26.ebuild \| 25 ++++
17	.../files/bedops-2.4.26-respect-cxxflags.patch \| 138 +++++++++++++++++++++
18	sci-biology/bedops/metadata.xml \| 12 ++
19	3 files changed, 175 insertions(+)
20
21	diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
22	new file mode 100644
23	index 000000000..d281fbede
24	--- /dev/null
25	+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
26	@@ -0,0 +1,25 @@
27	+# Copyright 1999-2017 Gentoo Foundation
28	+# Distributed under the terms of the GNU General Public License v2
29	+
30	+EAPI=6
31	+
32	+inherit toolchain-funcs eutils
33	+
34	+DESCRIPTION="Manipulate BED file (alternative to bedtools)"
35	+HOMEPAGE="http://bedops.readthedocs.io
36	+ https://github.com/bedops/bedops"
37	+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
38	+
39	+LICENSE="GPL-2"
40	+SLOT="0"
41	+KEYWORDS="~amd64 ~x86"
42	+IUSE=""
43	+
44	+DEPEND=""
45	+RDEPEND="${DEPEND}"
46	+
47	+src_prepare(){
48	+ default
49	+ local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
50	+ epatch ${PATCHES[@]}
51	+}
52
53	diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
54	new file mode 100644
55	index 000000000..16ac4e2b0
56	--- /dev/null
57	+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
58	@@ -0,0 +1,138 @@
59	+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
60	++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200
61	+@@ -28,7 +28,7 @@
62	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
63	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
64	+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
65	+-BLDFLAGS = -O3 ${STDFLAGS}
66	++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
67	+
68	+
69	+ 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} ${INCLUDES}
70	+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
71	++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200
72	+@@ -24,7 +24,7 @@
73	+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
74	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
75	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
76	+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
77	++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
78	+ SFLAGS = -static
79	+
80	+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
81	+@@ -64,4 +64,4 @@
82	+ rm -rf $(OBJDIR)
83	+ rm -f $(BINDIR)/$(PROG)
84	+ rm -f $(BINDIR)/*.$(PROG)
85	+- rm -rf $(BINDIR)
86	+\ No newline at end of file
87	++ rm -rf $(BINDIR)
88	+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
89	++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200
90	+@@ -28,7 +28,7 @@
91	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
92	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
93	+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
94	+-BLDFLAGS = -O3 ${STDFLAGS}
95	++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
96	+
97	+ 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} ${INCLUDES}
98	+
99	+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
100	++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200
101	+@@ -23,7 +23,7 @@
102	+ INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
103	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
104	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
105	+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
106	++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
107	+ SFLAGS = -static
108	+
109	+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
110	+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
111	++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200
112	+@@ -1,7 +1,7 @@
113	+ MIN_OSX_VERSION = 10.7
114	+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
115	+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
116	+-CFLAGS = -O3
117	++CFLAGS = ${CXXFLAGS:--O3}
118	+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
119	+ CPFLAGS = -pg
120	+ LIBS = -lpthread
121	+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
122	++++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200
123	+@@ -1,6 +1,6 @@
124	+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
125	+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
126	+-CFLAGS = -O3
127	++CFLAGS = ${CXXFLAGS:--O3}
128	+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
129	+ CPFLAGS = -pg
130	+ LIBS = -lpthread
131	+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
132	++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200
133	+@@ -27,7 +27,7 @@
134	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
135	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
136	+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
137	+-BLDFLAGS = -O3 ${STDFLAGS}
138	++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
139	+
140	+ 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} ${INCLUDES}
141	+
142	+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
143	++++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200
144	+@@ -25,7 +25,7 @@
145	+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
146	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
147	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
148	+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
149	++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
150	+ SFLAGS = -static
151	+
152	+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
153	+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
154	++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200
155	+@@ -28,7 +28,7 @@
156	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
157	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
158	+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
159	+-BLDFLAGS = -O3 ${STDFLAGS}
160	++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
161	+
162	+ 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} ${INCLUDES}
163	+
164	+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
165	++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200
166	+@@ -23,7 +23,7 @@
167	+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
168	+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
169	+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
170	+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
171	++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
172	+ SFLAGS = -static
173	+
174	+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
175	+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
176	++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200
177	+@@ -7,7 +7,7 @@
178	+ PROG = sort-bed
179	+ DIST_DIR = ../bin
180	+ OBJ_DIR = objects_${ARCH}
181	+-OPTIMIZE = -O3 -std=c++11 -stdlib=libc++
182	++OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
183	+ WARNINGS = -Wall
184	+ MAIN = ../../../..
185	+ HEAD = ${MAIN}/interfaces/general-headers
186	+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
187	++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200
188	+@@ -29,7 +29,7 @@
189	+ BINDIR = ../bin
190	+ OBJDIR = objects
191	+ WARNINGS = -Wall -Wextra -pedantic
192	+-BLDFLAGS = ${WARNINGS} -O3 -std=c++11
193	++BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
194	+ SFLAGS = -static
195	+
196	+ dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
197
198	diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml
199	new file mode 100644
200	index 000000000..f68a1b6fa
201	--- /dev/null
202	+++ b/sci-biology/bedops/metadata.xml
203	@@ -0,0 +1,12 @@
204	+<?xml version="1.0" encoding="UTF-8"?>
205	+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
206	+<pkgmetadata>
207	+ <maintainer type="person">
208	+ <email>mmokrejs@×××××××××××××××.cz</email>
209	+ <name>Martin Mokrejs</name>
210	+ </maintainer>
211	+ <maintainer type="project">
212	+ <email>sci-biology@g.o</email>
213	+ <name>Gentoo Biology Project</name>
214	+ </maintainer>
215	+</pkgmetadata>

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