CVS commit: pkgsrc/biology/biolibc

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Jun 11 17:04:55 UTC 2021

Modified Files:
        pkgsrc/biology/biolibc: Makefile PLIST buildlink3.mk distinfo

Log Message:
biology/biolibc: Update to 0.1.3

Import sam_buff_t class and VCF functions from ad2vcf
Add BED and GFF support
Isolate headers under include/biolibc
Numerous small enhancements and fixes

Upstream change log: https://github.com/auerlab/biolibc/releases


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/biolibc/Makefile \
    pkgsrc/biology/biolibc/PLIST pkgsrc/biology/biolibc/buildlink3.mk \
    pkgsrc/biology/biolibc/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/biolibc/Makefile
diff -u pkgsrc/biology/biolibc/Makefile:1.1 pkgsrc/biology/biolibc/Makefile:1.2
--- pkgsrc/biology/biolibc/Makefile:1.1 Wed Mar 24 15:20:08 2021
+++ pkgsrc/biology/biolibc/Makefile     Fri Jun 11 17:04:55 2021
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.1 2021/03/24 15:20:08 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2021/06/11 17:04:55 bacon Exp $
 
-DISTNAME=      biolibc-0.1.1
+DISTNAME=      biolibc-0.1.3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
 
@@ -9,4 +9,19 @@ HOMEPAGE=      https://github.com/auerlab/bio
 COMMENT=       Low-level high-performance bioinformatics library
 LICENSE=       2-clause-bsd
 
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == Darwin
+BUILD_TARGET=  apple
+INSTALL_TARGET=        apple-install
+.else
+INSTALL_TARGET=        install-strip
+.endif
+
+MAKE_ENV+=     DYLIB_PATH=${PREFIX}/lib
+
+pre-build:
+       cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend
+
+.include "../../devel/libxtend/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/biolibc/PLIST
diff -u pkgsrc/biology/biolibc/PLIST:1.1 pkgsrc/biology/biolibc/PLIST:1.2
--- pkgsrc/biology/biolibc/PLIST:1.1    Wed Mar 24 15:20:08 2021
+++ pkgsrc/biology/biolibc/PLIST        Fri Jun 11 17:04:55 2021
@@ -1,7 +1,29 @@
-@comment $NetBSD: PLIST,v 1.1 2021/03/24 15:20:08 bacon Exp $
-include/biostring.h
-include/dsvio.h
-include/samio.h
-include/vcfio.h
+@comment $NetBSD: PLIST,v 1.2 2021/06/11 17:04:55 bacon Exp $
+include/biolibc/bed.h
+include/biolibc/biolibc.h
+include/biolibc/dsv.h
+include/biolibc/gff.h
+include/biolibc/plist.h
+include/biolibc/sam-buff.h
+include/biolibc/sam.h
+include/biolibc/vcf.h
 lib/libbiolibc.a
-man/man1/biolibc.1
+lib/libbiolibc.so
+lib/libbiolibc.so.2
+lib/libbiolibc.so.2.0
+man/man3/bed_check_order.3
+man/man3/bed_gff_cmp.3
+man/man3/bed_read_feature.3
+man/man3/bed_set_chromosome.3
+man/man3/bed_set_end_pos.3
+man/man3/bed_set_fields.3
+man/man3/bed_set_name.3
+man/man3/bed_set_rgb_str.3
+man/man3/bed_set_score.3
+man/man3/bed_set_start_pos.3
+man/man3/bed_set_strand.3
+man/man3/bed_set_thick_end_pos.3
+man/man3/bed_set_thick_start_pos.3
+man/man3/bed_skip_header.3
+man/man3/bed_write_feature.3
+man/man3/biolibc.3
Index: pkgsrc/biology/biolibc/buildlink3.mk
diff -u pkgsrc/biology/biolibc/buildlink3.mk:1.1 pkgsrc/biology/biolibc/buildlink3.mk:1.2
--- pkgsrc/biology/biolibc/buildlink3.mk:1.1    Wed Mar 24 15:20:08 2021
+++ pkgsrc/biology/biolibc/buildlink3.mk        Fri Jun 11 17:04:55 2021
@@ -1,13 +1,12 @@
-# $NetBSD: buildlink3.mk,v 1.1 2021/03/24 15:20:08 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.2 2021/06/11 17:04:55 bacon Exp $
 
 BUILDLINK_TREE+=       biolibc
 
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.1.1
+BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.1.3
 BUILDLINK_PKGSRCDIR.biolibc?=  ../../biology/biolibc
-BUILDLINK_DEPMETHOD.biolibc?=  build
 .endif # BIOLIBC_BUILDLINK3_MK
 
 BUILDLINK_TREE+=       -biolibc
Index: pkgsrc/biology/biolibc/distinfo
diff -u pkgsrc/biology/biolibc/distinfo:1.1 pkgsrc/biology/biolibc/distinfo:1.2
--- pkgsrc/biology/biolibc/distinfo:1.1 Wed Mar 24 15:20:08 2021
+++ pkgsrc/biology/biolibc/distinfo     Fri Jun 11 17:04:55 2021
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2021/03/24 15:20:08 bacon Exp $
+$NetBSD: distinfo,v 1.2 2021/06/11 17:04:55 bacon Exp $
 
-SHA1 (biolibc-0.1.1.tar.gz) = 7c5861ebfd97dd6d92a489297244debe3c48af05
-RMD160 (biolibc-0.1.1.tar.gz) = 95b9fce0efe0c68be43bea5f875a72efce98f58e
-SHA512 (biolibc-0.1.1.tar.gz) = 673fa88ab48bbbcd5d3256a244472fdaa2c76fc5c0fa78663179487f8d8e9c65aaff593220859a54ed6e17f76a080cabe7e5866d12ab3948996e28b0d05d12bc
-Size (biolibc-0.1.1.tar.gz) = 11770 bytes
+SHA1 (biolibc-0.1.3.tar.gz) = e3381720674b2bc27ec4bfa9c0823fa2012d3422
+RMD160 (biolibc-0.1.3.tar.gz) = e857f91609d71ad6698534d5cf47c070c5538c94
+SHA512 (biolibc-0.1.3.tar.gz) = 92c08cfec13e99c33d2a275ce5dc69c0bd4160a2d7851c2693b3c825a95a0b6797adfd7ca606d70511b63c8e275ab635f88af8ad639556ebe318b1086b59ac3e
+Size (biolibc-0.1.3.tar.gz) = 30046 bytes