diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/kmcp/Makefile | 2 | ||||
| -rw-r--r-- | biology/megahit/Makefile | 8 | ||||
| -rw-r--r-- | biology/megahit/distinfo | 6 | ||||
| -rw-r--r-- | biology/ncbi-entrez-direct/Makefile | 2 | ||||
| -rw-r--r-- | biology/seqkit/Makefile | 2 | ||||
| -rw-r--r-- | biology/taxonkit/Makefile | 2 | ||||
| -rw-r--r-- | biology/unikmer/Makefile | 2 | ||||
| -rw-r--r-- | biology/vcflib/files/patch-src-zig-samples.zig | 31 |
8 files changed, 43 insertions, 12 deletions
diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile index d52bac6491ea..2936637408be 100644 --- a/biology/kmcp/Makefile +++ b/biology/kmcp/Makefile @@ -1,7 +1,7 @@ PORTNAME= kmcp DISTVERSIONPREFIX= v DISTVERSION= 0.9.4 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/megahit/Makefile b/biology/megahit/Makefile index 379440059baa..164ef21acf64 100644 --- a/biology/megahit/Makefile +++ b/biology/megahit/Makefile @@ -1,7 +1,7 @@ PORTNAME= megahit DISTVERSIONPREFIX= v -DISTVERSION= 1.2.9 -PORTREVISION= 1 +DISTVERSION= 1.2.9-20 +DISTVERSIONSUFFIX= -g3821b10 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,8 +11,8 @@ WWW= https://github.com/voutcn/megahit LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE -ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le riscv64 -ONLY_FOR_ARCHS_REASON= "Uses specific 64-bit CPU features" +ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64 +ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor USES= cmake python shebangfix SHEBANG_FILES= src/megahit diff --git a/biology/megahit/distinfo b/biology/megahit/distinfo index a70a74294d7a..eaf38afd5db0 100644 --- a/biology/megahit/distinfo +++ b/biology/megahit/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1669058254 -SHA256 (voutcn-megahit-v1.2.9_GH0.tar.gz) = 09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852 -SIZE (voutcn-megahit-v1.2.9_GH0.tar.gz) = 268591 +TIMESTAMP = 1748000175 +SHA256 (voutcn-megahit-v1.2.9-20-g3821b10_GH0.tar.gz) = 743d45843a4fb58134c1e68e5d5e0987320bc3dfa949f1ab6e719b78d1f317fa +SIZE (voutcn-megahit-v1.2.9-20-g3821b10_GH0.tar.gz) = 268974 diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index 43ccbb2354ba..8e02ebac7423 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -1,6 +1,6 @@ PORTNAME= ncbi-entrez-direct DISTVERSION= 14.9.20210423 -PORTREVISION= 26 +PORTREVISION= 27 CATEGORIES= biology perl5 MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/ DISTFILES= edirect.tar.gz diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile index 2d1577a4a940..3cd8e1318a0e 100644 --- a/biology/seqkit/Makefile +++ b/biology/seqkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= seqkit DISTVERSIONPREFIX= v DISTVERSION= 2.10.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile index dfe61730aaee..fe4b34852a71 100644 --- a/biology/taxonkit/Makefile +++ b/biology/taxonkit/Makefile @@ -1,7 +1,7 @@ PORTNAME= taxonkit DISTVERSIONPREFIX= v DISTVERSION= 0.19.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile index 364d635628d0..4d571776c94e 100644 --- a/biology/unikmer/Makefile +++ b/biology/unikmer/Makefile @@ -1,7 +1,7 @@ PORTNAME= unikmer DISTVERSIONPREFIX= v DISTVERSION= 0.20.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/vcflib/files/patch-src-zig-samples.zig b/biology/vcflib/files/patch-src-zig-samples.zig new file mode 100644 index 000000000000..e69584b175e0 --- /dev/null +++ b/biology/vcflib/files/patch-src-zig-samples.zig @@ -0,0 +1,31 @@ +diff --git src/zig/samples.zig src/zig/samples.zig +index cb05a1f2..ccd5b149 100644 +--- src/zig/samples.zig ++++ src/zig/samples.zig +@@ -28,7 +28,11 @@ const GENOTYPE_MISSING = -256; + fn split_samples(str: []const u8) *ArrayList([] const u8) { + var list = ArrayList([] const u8).init(allocator); + defer list.deinit(); +- var splits = std.mem.split(u8, str, " "); ++ ++ var splits = if (@hasDecl(std.mem, "splitScalar")) ++ std.mem.splitScalar(u8, str, ' ') ++ else ++ std.mem.split(u8, str, ' '); + while (splits.next()) |chunk| { + list.append(chunk) catch |err| { + std.debug.print("out of memory {}\n", .{err}); +@@ -61,10 +65,10 @@ const Genotypes = struct { + fn to_num(str: []const u8) !ArrayList(i64) { + var list = ArrayList(i64).init(allocator); + +- var splits = if (is_phased(str)) +- std.mem.split(u8, str, "|") ++ var splits = if (@hasDecl(std.mem, "splitScalar")) ++ std.mem.splitScalar(u8, str, if (is_phased(str)) '|' else '/') + else +- std.mem.split(u8, str, "/"); ++ std.mem.split(u8, str, if (is_phased(str)) '|' else '/' ); + + while (splits.next()) |chunk| { + const i: i64 = |