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-rw-r--r--biology/bifrost/Makefile12
-rw-r--r--biology/bifrost/distinfo2
-rw-r--r--biology/bifrost/files/patch-src_DataStorage.tcc14
-rw-r--r--biology/fasda/Makefile3
-rw-r--r--biology/fasda/distinfo6
-rw-r--r--biology/kallisto/Makefile12
-rw-r--r--biology/kallisto/distinfo2
-rw-r--r--biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc14
-rw-r--r--biology/kmcp/Makefile2
-rw-r--r--biology/megahit/Makefile8
-rw-r--r--biology/megahit/distinfo6
-rw-r--r--biology/ncbi-entrez-direct/Makefile2
-rw-r--r--biology/p5-TrimGalore/Makefile2
-rw-r--r--biology/seqkit/Makefile2
-rw-r--r--biology/taxonkit/Makefile2
-rw-r--r--biology/unikmer/Makefile2
16 files changed, 52 insertions, 39 deletions
diff --git a/biology/bifrost/Makefile b/biology/bifrost/Makefile
index 082d27df32e6..e1873b430549 100644
--- a/biology/bifrost/Makefile
+++ b/biology/bifrost/Makefile
@@ -1,6 +1,7 @@
PORTNAME= bifrost
DISTVERSIONPREFIX= v
DISTVERSION= 1.3.5
+PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@@ -22,13 +23,4 @@ CXXFLAGS+= -Wno-unqualified-std-cast-call
GH_ACCOUNT= pmelsted
-.include <bsd.port.pre.mk>
-
-# Build fails with clang19, but succeeds with gcc13
-# Have not figured out where this sz_link member is even supposed to come from
-# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
-.if ${OSVERSION} > 1500000
-USE_GCC= yes
-.endif
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/bifrost/distinfo b/biology/bifrost/distinfo
index 49f7e2d919bb..43195678b9c9 100644
--- a/biology/bifrost/distinfo
+++ b/biology/bifrost/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1710590640
+TIMESTAMP = 1748282354
SHA256 (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341
SIZE (pmelsted-bifrost-v1.3.5_GH0.tar.gz) = 356701
diff --git a/biology/bifrost/files/patch-src_DataStorage.tcc b/biology/bifrost/files/patch-src_DataStorage.tcc
new file mode 100644
index 000000000000..22196bb8e11c
--- /dev/null
+++ b/biology/bifrost/files/patch-src_DataStorage.tcc
@@ -0,0 +1,14 @@
+--- src/DataStorage.tcc.orig 2024-03-15 15:20:17 UTC
++++ src/DataStorage.tcc
+@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataStorage& o) : co
+
+ unitig_cs_link = new atomic<uint64_t>[sz_link];
+
+- for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++ // Hayzam Sherif: o.sz_link -> o.unitig_cs_link
++ // Independently proposed by Lucas van Dijk:
++ // https://github.com/pmelsted/bifrost/pull/18/files
++ for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+ }
+
+ if ((o.data != nullptr) && (o.sz_cs != 0)){
diff --git a/biology/fasda/Makefile b/biology/fasda/Makefile
index 90af1fc205cb..2d85a23af573 100644
--- a/biology/fasda/Makefile
+++ b/biology/fasda/Makefile
@@ -1,5 +1,6 @@
PORTNAME= fasda
-DISTVERSION= 0.2.0
+DISTVERSION= 0.2.0-1
+DISTVERSIONSUFFIX= -ga7d14ad
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/fasda/distinfo b/biology/fasda/distinfo
index f7174b017086..ad561981d758 100644
--- a/biology/fasda/distinfo
+++ b/biology/fasda/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1745682225
-SHA256 (auerlab-fasda-0.2.0_GH0.tar.gz) = 5e52e9773d70b4ffa303b91a3e156cfc706e738b3fc17503d20bfbbaefd82446
-SIZE (auerlab-fasda-0.2.0_GH0.tar.gz) = 1869574
+TIMESTAMP = 1748181140
+SHA256 (auerlab-fasda-0.2.0-1-ga7d14ad_GH0.tar.gz) = fbc12198337617a2f09a95fda627861e8ed7fa2f345ccee218879b5c58cabea7
+SIZE (auerlab-fasda-0.2.0-1-ga7d14ad_GH0.tar.gz) = 1869807
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index c2d33ef3ce82..ee2b20397ca6 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,6 +1,7 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
DISTVERSION= 0.51.1
+PORTREVISION= 1
PORTEPOCH= 1
CATEGORIES= biology
@@ -42,17 +43,8 @@ LDFLAGS+= -lhts -lz
OPTIONS_DEFINE= EXAMPLES
-.include <bsd.port.pre.mk>
-
-# Build fails with clang19, but succeeds with gcc13
-# Have not figured out where this sz_link member is even supposed to come from
-# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
-.if ${OSVERSION} > 1500000
-USE_GCC= yes
-.endif
-
post-install-EXAMPLES-on:
${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index 98b8775d9539..a207db3e922d 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1726658334
+TIMESTAMP = 1748283025
SHA256 (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516
SIZE (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = 5954250
diff --git a/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc b/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc
new file mode 100644
index 000000000000..0e6dcb8cca18
--- /dev/null
+++ b/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc
@@ -0,0 +1,14 @@
+--- ext/bifrost/src/DataStorage.tcc.orig 2024-09-17 05:40:08 UTC
++++ ext/bifrost/src/DataStorage.tcc
+@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataStorage& o) : co
+
+ unitig_cs_link = new atomic<uint64_t>[sz_link];
+
+- for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++ // Hayzam Sherif: o.sz_link -> o.unitig_cs_link
++ // Independently proposed by Lucas van Dijk:
++ // https://github.com/pmelsted/bifrost/pull/18/files
++ for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+ }
+
+ if ((o.data != nullptr) && (o.sz_cs != 0)){
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/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile
index 8b6e229c0032..cd7a5cf7ffe7 100644
--- a/biology/p5-TrimGalore/Makefile
+++ b/biology/p5-TrimGalore/Makefile
@@ -3,7 +3,7 @@ DISTVERSION= 0.6.10
CATEGORIES= biology perl5 python
PKGNAMEPREFIX= p5-
-MAINTAINER= ports@FreeBSD.org
+MAINTAINER= perl@FreeBSD.org
COMMENT= Wrapper around Cutadapt and FastQC for adapter and quality trimming
WWW= https://github.com/FelixKrueger/TrimGalore
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
generated by cgit v1.2.3 (git 2.25.1) at 2025-06-13 11:59:49 +0000