Fix build against newer protocol buffers library. Regenerate source from missing protocol description fetched from: https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/variant.proto https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/pp.proto Bump PKGREVISION.diff -r1.1 -r1.2 pkgsrc/biology/plinkseq/Makefile
(asau)
@@ -1,25 +1,36 @@ | @@ -1,25 +1,36 @@ | |||
1 | # $NetBSD: Makefile,v 1.1 2012/11/01 04:06:21 asau Exp $ | 1 | # $NetBSD: Makefile,v 1.2 2013/03/26 20:11:19 asau Exp $ | |
2 | 2 | |||
3 | DISTNAME= plinkseq-0.08 | 3 | DISTNAME= plinkseq-0.08 | |
4 | PKGREVISION= 1 | |||
4 | CATEGORIES= biology | 5 | CATEGORIES= biology | |
5 | MASTER_SITES= http://atgu.mgh.harvard.edu/plinkseq/dist/version-0.08/ | 6 | MASTER_SITES= http://atgu.mgh.harvard.edu/plinkseq/dist/version-0.08/ | |
6 | 7 | |||
7 | MAINTAINER= jwbacon@tds.net | 8 | MAINTAINER= jwbacon@tds.net | |
8 | HOMEPAGE= http://atgu.mgh.harvard.edu/plinkseq/ | 9 | HOMEPAGE= http://atgu.mgh.harvard.edu/plinkseq/ | |
9 | COMMENT= C/C++ library for working with human genetic variation data | 10 | COMMENT= C/C++ library for working with human genetic variation data | |
10 | LICENSE= gnu-gpl-v2 # Assuming same as plink. No info on web. | 11 | LICENSE= gnu-gpl-v2 # Assuming same as plink. No info on web. | |
11 | 12 | |||
12 | GNU_CONFIGURE= yes | 13 | GNU_CONFIGURE= yes | |
13 | USE_LIBTOOL= yes | 14 | USE_LIBTOOL= yes | |
14 | USE_LANGUAGES= c c++ | 15 | USE_LANGUAGES= c c++ | |
15 | USE_TOOLS= bash:run | 16 | USE_TOOLS= bash:run | |
16 | REPLACE_BASH= browser/pbrowse.in index/index.in | 17 | REPLACE_BASH= browser/pbrowse.in index/index.in | |
17 | 18 | |||
18 | .include "../../mk/bsd.prefs.mk" | 19 | .include "../../mk/bsd.prefs.mk" | |
19 | 20 | |||
20 | .if $(OPSYS) != "Linux" | 21 | .if $(OPSYS) != "Linux" | |
21 | BUILDLINK_TRANSFORM= rm:-ldl | 22 | BUILDLINK_TRANSFORM= rm:-ldl | |
22 | .endif | 23 | .endif | |
23 | 24 | |||
25 | # Put missing protocol description files in place: | |||
26 | post-extract: | |||
27 | $(CP) $(FILESDIR)/pp.proto $(WRKSRC)/lib/ | |||
28 | $(CP) $(FILESDIR)/variant.proto $(WRKSRC)/lib/ | |||
29 | ||||
30 | # Regenerate: | |||
31 | pre-build: | |||
32 | cd $(WRKSRC)/lib && protoc --cpp_out=. pp.proto && mv pp.pb.cc pp.pb.cpp | |||
33 | cd $(WRKSRC)/lib && protoc --cpp_out=. variant.proto && mv variant.pb.cc variant.pb.cpp | |||
34 | ||||
24 | .include "../../devel/protobuf/buildlink3.mk" | 35 | .include "../../devel/protobuf/buildlink3.mk" | |
25 | .include "../../mk/bsd.pkg.mk" | 36 | .include "../../mk/bsd.pkg.mk" |
message PolyPhen2Buffer {
enum pred_t { UNKNOWN = 0; BENIGN = 1; POSS = 2; PROB = 3; }
required string transcript_name = 1;
required string protein_name = 2;
repeated int32 position = 3 [packed=true];
repeated string reference = 4;
repeated string alternate = 5;
repeated double score = 6 [packed=true];
repeated pred_t prediction = 7 [packed=true];
}
message VariantMetaUnit {
enum Type { INT = 1; FLOAT = 2; TEXT = 3; BOOL = 4; }
required Type type = 1;
required string name = 2;
repeated int32 int_value = 3 [packed=true];
repeated double double_value = 4 [packed=true];
repeated string string_value = 5;
repeated bool bool_value = 6 [packed=true];
}
message GenotypeMetaUnit {
enum Type { INT = 1; FLOAT = 2; TEXT = 3; BOOL = 4; }
required Type type = 1;
required string name = 2;
optional int32 fixed_len = 3;
repeated int32 len = 4 [packed=true];
repeated int32 int_value = 5 [packed=true];
repeated double double_value = 6 [packed=true];
repeated string string_value = 7;
repeated bool bool_value = 8 [packed=true];
optional int32 fixed_indiv = 9;
repeated int32 indiv_index = 10 [packed=true];
repeated int32 missing_index = 11 [packed=true];
}
message VariantBuffer {
optional string ref = 1;
optional string alt = 2;
optional double quality = 3;
repeated string filter = 4;
}
message VariantMetaBuffer {
repeated VariantMetaUnit vmeta = 1;
}
message GenotypeBuffer {
repeated uint32 geno = 1 [packed=true];
}
message GenotypeMetaBuffer {
repeated GenotypeMetaUnit gmeta = 1;
}