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-rw-r--r--biology/R-cran-BiocManager/Makefile2
-rw-r--r--biology/R-cran-BiocManager/distinfo6
-rw-r--r--biology/biostar-tools/Makefile4
-rw-r--r--biology/biostar-tools/distinfo2
-rw-r--r--biology/coverm/Makefile2
-rw-r--r--biology/hyphy/Makefile2
-rw-r--r--biology/hyphy/distinfo6
-rw-r--r--biology/iqtree/Makefile9
-rw-r--r--biology/iqtree/distinfo10
-rw-r--r--biology/salmon/Makefile1
-rw-r--r--biology/seqkit/Makefile2
-rw-r--r--biology/sra-tools/Makefile2
-rw-r--r--biology/sra-tools/distinfo10
-rw-r--r--biology/sra-tools/files/patch-libs_kxml_xml.c11
-rw-r--r--biology/sra-tools/pkg-plist4
-rw-r--r--biology/vcflib/Makefile2
-rw-r--r--biology/vsearch/Makefile2
-rw-r--r--biology/vsearch/distinfo6
-rw-r--r--biology/vsearch/files/patch-src_arch.cc32
19 files changed, 79 insertions, 36 deletions
diff --git a/biology/R-cran-BiocManager/Makefile b/biology/R-cran-BiocManager/Makefile
index 09af6b32ebbd..4108598eb89c 100644
--- a/biology/R-cran-BiocManager/Makefile
+++ b/biology/R-cran-BiocManager/Makefile
@@ -1,5 +1,5 @@
PORTNAME= BiocManager
-DISTVERSION= 1.30.26
+DISTVERSION= 1.30.27
CATEGORIES= biology
DISTNAME= ${PORTNAME}_${DISTVERSION}
diff --git a/biology/R-cran-BiocManager/distinfo b/biology/R-cran-BiocManager/distinfo
index 641e60aea07f..4e20ca105cd7 100644
--- a/biology/R-cran-BiocManager/distinfo
+++ b/biology/R-cran-BiocManager/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1750881870
-SHA256 (BiocManager_1.30.26.tar.gz) = db9a67556f8f46f41a86dc2abb2c19d354cdf537d4a1b48132896946eb45a23e
-SIZE (BiocManager_1.30.26.tar.gz) = 594489
+TIMESTAMP = 1766018294
+SHA256 (BiocManager_1.30.27.tar.gz) = acbfdcf09602c8279085556ca54531c2ada0ac3c1775d54ce2c3b9a3dc03fbb5
+SIZE (BiocManager_1.30.27.tar.gz) = 752490
diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile
index 2be07b115d09..a064727f9217 100644
--- a/biology/biostar-tools/Makefile
+++ b/biology/biostar-tools/Makefile
@@ -1,6 +1,5 @@
PORTNAME= biostar-tools
-PORTVERSION= 2.0
-PORTREVISION= 1
+PORTVERSION= 2.1
CATEGORIES= biology python
MASTER_SITES= # empty
@@ -23,7 +22,6 @@ RUN_DEPENDS= wget>0:ftp/wget \
miller>0:textproc/miller \
ncbi-entrez-direct>0:biology/ncbi-entrez-direct \
readseq>0:biology/readseq \
- snpeff>0:biology/snpeff \
picard-tools>0:biology/picard-tools \
bbmap>0:biology/bbmap \
minimap2>0:biology/minimap2 \
diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo
index 4bfd994ffd70..5dbd4683d58b 100644
--- a/biology/biostar-tools/distinfo
+++ b/biology/biostar-tools/distinfo
@@ -1 +1 @@
-TIMESTAMP = 1731026515
+TIMESTAMP = 1766068787
diff --git a/biology/coverm/Makefile b/biology/coverm/Makefile
index 937e6b6ba23b..9683f8b270a6 100644
--- a/biology/coverm/Makefile
+++ b/biology/coverm/Makefile
@@ -1,7 +1,7 @@
PORTNAME= coverm
DISTVERSIONPREFIX= v
DISTVERSION= 0.7.0
-PORTREVISION= 10
+PORTREVISION= 11
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 162685dfa948..0da9c95b5c87 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
PORTNAME= hyphy
-DISTVERSION= 2.5.88
+DISTVERSION= 2.5.90
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index 7c94400e376d..2c0ccc9928ee 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1765067195
-SHA256 (veg-hyphy-2.5.88_GH0.tar.gz) = 0122f793fdf68599b96162dfea6a7fc34484c1d1a5dce8819d5b8d032878dba6
-SIZE (veg-hyphy-2.5.88_GH0.tar.gz) = 4372610
+TIMESTAMP = 1765759320
+SHA256 (veg-hyphy-2.5.90_GH0.tar.gz) = d11f7ce637c0683ffb253a4c371fd9ed9bdb70e5513fc4cb3c50546782012173
+SIZE (veg-hyphy-2.5.90_GH0.tar.gz) = 4372927
diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile
index 6d4837298edc..af11d67a7c5a 100644
--- a/biology/iqtree/Makefile
+++ b/biology/iqtree/Makefile
@@ -1,7 +1,6 @@
PORTNAME= iqtree
DISTVERSIONPREFIX= v
-DISTVERSION= 2.4.0
-PORTREVISION= 3
+DISTVERSION= 3.0.1
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
@@ -20,9 +19,9 @@ LIB_DEPENDS= libboost_filesystem.so:devel/boost-libs
USES= cmake eigen:3
USE_GITHUB= yes
-GH_PROJECT= iqtree2
+GH_PROJECT= iqtree3
GH_TUPLE= tothuhien:lsd2:c61110f3a4fa05325b45c97b2134792ff9d55d4c:tothuhien/lsd2 \
- iqtree:cmaple:3946f47731699573ed2268e00aa7996a3458d4eb:iqtree/cmaple
+ iqtree:cmaple:29df93e77b7ad159b19e8cdd8150545baa1221ae:iqtree/cmaple
PLIST_FILES= bin/iqtree
PORTEXAMPLES= custom_distributions.txt example.cf example.nex example.phy \
@@ -31,7 +30,7 @@ PORTEXAMPLES= custom_distributions.txt example.cf example.nex example.phy \
OPTIONS_DEFINE= EXAMPLES
do-install:
- ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iqtree2 ${STAGEDIR}${PREFIX}/bin/iqtree
+ ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iqtree3 ${STAGEDIR}${PREFIX}/bin/iqtree
do-install-EXAMPLES-on:
@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
diff --git a/biology/iqtree/distinfo b/biology/iqtree/distinfo
index ae72ac55ee39..f42a38d7c5f0 100644
--- a/biology/iqtree/distinfo
+++ b/biology/iqtree/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1739123157
-SHA256 (iqtree-iqtree2-v2.4.0_GH0.tar.gz) = 06a3351de0ed3c44a3e197e94a5d0cc3de7359c0be79eab1f41fb83459234619
-SIZE (iqtree-iqtree2-v2.4.0_GH0.tar.gz) = 5524827
+TIMESTAMP = 1765767206
+SHA256 (iqtree-iqtree3-v3.0.1_GH0.tar.gz) = 2daff8eaa24faaeac3dee9ac63af9fd7b79cc94cf7031671f0068b051b12c55f
+SIZE (iqtree-iqtree3-v3.0.1_GH0.tar.gz) = 5172154
SHA256 (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 9bbeaa0f8f35783c1d8dec74df6c93a804dbca808fa04484f9123de4e7258b53
SIZE (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 1529381
-SHA256 (iqtree-cmaple-3946f47731699573ed2268e00aa7996a3458d4eb_GH0.tar.gz) = 712016835e40c26c1e69529fca1bec46a7102ede3775e1b4b6589c4b6074410a
-SIZE (iqtree-cmaple-3946f47731699573ed2268e00aa7996a3458d4eb_GH0.tar.gz) = 4806755
+SHA256 (iqtree-cmaple-29df93e77b7ad159b19e8cdd8150545baa1221ae_GH0.tar.gz) = f8b5115823614b4c710a13ded1b38b59953c9f3127ced46246d1a4b1db026e37
+SIZE (iqtree-cmaple-29df93e77b7ad159b19e8cdd8150545baa1221ae_GH0.tar.gz) = 4807064
diff --git a/biology/salmon/Makefile b/biology/salmon/Makefile
index 1b042365ed13..7097ee7a77df 100644
--- a/biology/salmon/Makefile
+++ b/biology/salmon/Makefile
@@ -46,7 +46,6 @@ CMAKE_ARGS+= -DHAVE_FAST_MALLOC:BOOL=on \
-DFETCHED_PUFFERFISH:BOOL=on \
-DFETCHED_LIBGFF:BOOL=on \
-DFETCH_STADEN:BOOL=true
-WITH_DEBUG= yes
CXXFLAGS+= -I${LOCALBASE}/include/eigen3
LDFLAGS+= -lpthread
diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile
index b818ac8e60c2..de47b892619c 100644
--- a/biology/seqkit/Makefile
+++ b/biology/seqkit/Makefile
@@ -12,7 +12,7 @@ WWW= https://bioinf.shenwei.me/seqkit \
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
-USES= go:1.24,modules
+USES= go:1.24+,modules
USE_GITHUB= nodefault
GH_TUPLE= golang:sys:v0.6.0:sys
diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index 3fa9ae25ebeb..b272f6b61534 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -1,5 +1,5 @@
PORTNAME= sra-tools
-DISTVERSION= 3.2.1
+DISTVERSION= 3.3.0
CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo
index d74965cf7e1a..5897b65aa802 100644
--- a/biology/sra-tools/distinfo
+++ b/biology/sra-tools/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1742507022
-SHA256 (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 2558683c217ad2318833ab7731939617ed91dc79a6b1dee92bf88b56a1dc142a
-SIZE (ncbi-sra-tools-3.2.1_GH0.tar.gz) = 66684089
-SHA256 (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 535511984928ec5bac02a61fc6b4d1ca72a5b69c742f4882eabd32ed3a97621c
-SIZE (ncbi-ncbi-vdb-3.2.1_GH0.tar.gz) = 19061776
+TIMESTAMP = 1765984755
+SHA256 (ncbi-sra-tools-3.3.0_GH0.tar.gz) = 3bfa26c5499a94d3b2a98eb65113bbb902f51dadef767c7c7247fc0175885a9a
+SIZE (ncbi-sra-tools-3.3.0_GH0.tar.gz) = 66485758
+SHA256 (ncbi-ncbi-vdb-3.3.0_GH0.tar.gz) = 36b3467affd53bea794e3eeb5598619d820bc726dc68751a189181ac7973047d
+SIZE (ncbi-ncbi-vdb-3.3.0_GH0.tar.gz) = 19055705
diff --git a/biology/sra-tools/files/patch-libs_kxml_xml.c b/biology/sra-tools/files/patch-libs_kxml_xml.c
new file mode 100644
index 000000000000..76ec7a13fee4
--- /dev/null
+++ b/biology/sra-tools/files/patch-libs_kxml_xml.c
@@ -0,0 +1,11 @@
+--- libs/kxml/xml.c.orig 2025-12-03 13:29:03 UTC
++++ libs/kxml/xml.c
+@@ -171,7 +171,7 @@ rc_t KXMLMgrSchemaValidate ( const KXMLMgr *self,
+ }
+ #endif
+
+-static void s_xmlGenericErrorDefaultFunc(void *ctx ATTRIBUTE_UNUSED,
++static void s_xmlGenericErrorDefaultFunc(void *ctx,
+ const char *msg,
+ ...)
+ {
diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist
index e047e75fdafd..0bc4898e1af5 100644
--- a/biology/sra-tools/pkg-plist
+++ b/biology/sra-tools/pkg-plist
@@ -181,6 +181,10 @@ jar/ngs-doc.jar
jar/ngs-examples.jar
jar/ngs-java.jar
jar/ngs-src.jar
+lib64/libkapp-static.a
+lib64/libkapp.a
+lib64/libkapp.a.3
+lib64/libkapp.a.%%PORTVERSION%%
lib64/libncbi-ngs-c++-static.a
lib64/libncbi-ngs-c++.a
lib64/libncbi-ngs-c++.a.3
diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index ac8ea593cdfa..e9538ba6e046 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -40,7 +40,7 @@ OPTIONS_SUB= yes
ZIG_DESC= Include Zig language support
-ZIG_BUILD_DEPENDS= zig>0:lang/zig
+ZIG_BUILD_DEPENDS= zig014=0.14.0:lang/zig014
CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0 \
-DTABIXPP_LOCAL=${WRKSRC}/contrib/tabixpp
diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index 897c01f7477d..54f34f6f2c93 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -1,6 +1,6 @@
PORTNAME= vsearch
DISTVERSIONPREFIX= v
-DISTVERSION= 2.30.1
+DISTVERSION= 2.30.2
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index c124a6bce96e..fa8f653b59b7 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1759667807
-SHA256 (torognes-vsearch-v2.30.1_GH0.tar.gz) = f65f03538a77cd1212bd04a52bb722114765329e64bd35e10ee2aefcd81137fe
-SIZE (torognes-vsearch-v2.30.1_GH0.tar.gz) = 334663
+TIMESTAMP = 1766069466
+SHA256 (torognes-vsearch-v2.30.2_GH0.tar.gz) = f4c244d2b48637e9a42325901b832ca5b6522cec8e2006b0da2aa9b9a0b5e699
+SIZE (torognes-vsearch-v2.30.2_GH0.tar.gz) = 334780
diff --git a/biology/vsearch/files/patch-src_arch.cc b/biology/vsearch/files/patch-src_arch.cc
new file mode 100644
index 000000000000..bf8d2e77dda7
--- /dev/null
+++ b/biology/vsearch/files/patch-src_arch.cc
@@ -0,0 +1,32 @@
+--- src/arch.cc.orig 2025-12-20 13:37:07 UTC
++++ src/arch.cc
+@@ -67,7 +67,7 @@
+ #include <cstdlib> // std::realloc, std::free
+
+
+-constexpr auto memalignment = 16;
++constexpr auto vsearch_memalignment = 16;
+
+
+ auto arch_get_memused() -> uint64_t
+@@ -223,9 +223,9 @@ auto xmalloc(std::size_t size) -> void *
+ size = std::max(size, minimal_allocation);
+ void * ptr = nullptr;
+ #ifdef _WIN32
+- ptr = _aligned_malloc(size, memalignment);
++ ptr = _aligned_malloc(size, vsearch_memalignment);
+ #else
+- if (posix_memalign(&ptr, memalignment, size) != 0)
++ if (posix_memalign(&ptr, vsearch_memalignment, size) != 0)
+ {
+ ptr = nullptr;
+ }
+@@ -243,7 +243,7 @@ auto xrealloc(void * ptr, std::size_t size) -> void *
+ static constexpr auto minimal_allocation = std::size_t{1};
+ size = std::max(size, minimal_allocation);
+ #ifdef _WIN32
+- void * new_ptr = _aligned_realloc(ptr, size, memalignment);
++ void * new_ptr = _aligned_realloc(ptr, size, vsearch_memalignment);
+ #else
+ void * new_ptr = realloc(ptr, size);
+ #endif
generated by cgit v1.2.3 (git 2.25.1) at 2025-12-23 11:22:01 +0000