summaryrefslogtreecommitdiff
path: root/science
diff options
context:
space:
mode:
Diffstat (limited to 'science')
-rw-r--r--science/cdo/Makefile2
-rw-r--r--science/colt/Makefile3
-rw-r--r--science/libkml/Makefile2
-rw-r--r--science/netcdf-cxx/Makefile2
-rw-r--r--science/netcdf-fortran/Makefile2
-rw-r--r--science/netcdf/Makefile2
-rw-r--r--science/opsin/Makefile1
-rw-r--r--science/opsin/files/patch-pom.xml22
-rw-r--r--science/pnetcdf/Makefile2
-rw-r--r--science/py-pyked/Makefile4
-rw-r--r--science/py-qiskit/Makefile2
-rw-r--r--science/tinker/Makefile2
-rw-r--r--science/tinker/distinfo6
-rw-r--r--science/tinker/pkg-plist10
14 files changed, 47 insertions, 15 deletions
diff --git a/science/cdo/Makefile b/science/cdo/Makefile
index d1bdbc708e93..ee01054d2e79 100644
--- a/science/cdo/Makefile
+++ b/science/cdo/Makefile
@@ -12,7 +12,7 @@ WWW= https://code.mpimet.mpg.de/projects/cdo
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE
-USES= compiler:c++20-lang gmake libtool localbase pathfix python:build
+USES= compiler:c++20-lang gmake libtool localbase python:build
CONFIGURE_ARGS= --disable-data \
--disable-extra \
diff --git a/science/colt/Makefile b/science/colt/Makefile
index 3304c3a6cb50..6edfe26a7c90 100644
--- a/science/colt/Makefile
+++ b/science/colt/Makefile
@@ -8,6 +8,9 @@ MAINTAINER= ports@FreeBSD.org
COMMENT= Java package for scalable scientific and technical computing
WWW= https://acs.lbl.gov/~hoschek/colt/
+DEPRECATED= java 8 only, unmaintained, no users in the ports tree, latest release was 2004
+EXPIRATION_DATE= 2026-04-13
+
JAVA_VERSION= 8
NO_ARCH= yes
diff --git a/science/libkml/Makefile b/science/libkml/Makefile
index 4f393b67245b..2e708f9c4b29 100644
--- a/science/libkml/Makefile
+++ b/science/libkml/Makefile
@@ -14,7 +14,7 @@ LIB_DEPENDS= libboost_thread.so:devel/boost-libs \
libexpat.so:textproc/expat2 \
liburiparser.so:net/uriparser
-USES= cmake compiler:c++11-lang minizip pathfix
+USES= cmake compiler:c++11-lang minizip
CMAKE_ARGS= -DEXPAT_LIBRARY=${LOCALBASE}/lib/libexpat.so
CMAKE_OFF= BUILD_TESTING WITH_JAVA WITH_PYTHON WITH_SWIG
diff --git a/science/netcdf-cxx/Makefile b/science/netcdf-cxx/Makefile
index d8c9f9934e3c..c27657275990 100644
--- a/science/netcdf-cxx/Makefile
+++ b/science/netcdf-cxx/Makefile
@@ -18,7 +18,7 @@ LICENSE_PERMS= auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
LIB_DEPENDS= libnetcdf.so:science/netcdf
-USES= libtool localbase pathfix
+USES= libtool localbase
CPPFLAGS+= -fPIC -DPIC
GNU_CONFIGURE= yes
diff --git a/science/netcdf-fortran/Makefile b/science/netcdf-fortran/Makefile
index ecb9a52e7e52..b3f9cb96f91b 100644
--- a/science/netcdf-fortran/Makefile
+++ b/science/netcdf-fortran/Makefile
@@ -17,7 +17,7 @@ LICENSE_PERMS= auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
BUILD_DEPENDS= netcdf>=4.9.0:science/netcdf
LIB_DEPENDS= libnetcdf.so:science/netcdf
-USES= fortran gmake libtool localbase makeinfo pathfix
+USES= fortran gmake libtool localbase makeinfo
CPPFLAGS+= -fPIC -DPIC -DgFortran
GNU_CONFIGURE= yes
diff --git a/science/netcdf/Makefile b/science/netcdf/Makefile
index c241bd9f7d5a..0fe19a3a0cd0 100644
--- a/science/netcdf/Makefile
+++ b/science/netcdf/Makefile
@@ -17,7 +17,7 @@ LIB_DEPENDS= libcurl.so:ftp/curl \
libhdf5.so:science/hdf5 \
libzstd.so:archivers/zstd
-USES= gmake libtool localbase ncurses pathfix pkgconfig:run
+USES= gmake libtool localbase ncurses pkgconfig:run
CONFIGURE_ARGS= --disable-filter-testing --disable-libxml2 \
--enable-byterange --enable-curl --enable-dap --enable-hdf5 --enable-logging
diff --git a/science/opsin/Makefile b/science/opsin/Makefile
index f4e98275bd30..b9c6e1f5da9d 100644
--- a/science/opsin/Makefile
+++ b/science/opsin/Makefile
@@ -15,7 +15,6 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt
BUILD_DEPENDS= maven>0:devel/maven
USES= java
-JAVA_VERSION= 17 # Java 8 fails on aarch64: Internal Error (assembler_aarch64.hpp:237), pid=29730, tid=0x000000000002d236 guarantee(val < (1U << nbits)) failed: Field too big for insn
NO_ARCH= yes
diff --git a/science/opsin/files/patch-pom.xml b/science/opsin/files/patch-pom.xml
new file mode 100644
index 000000000000..97c13f852077
--- /dev/null
+++ b/science/opsin/files/patch-pom.xml
@@ -0,0 +1,22 @@
+--- pom.xml.orig 2025-12-13 15:51:13 UTC
++++ pom.xml
+@@ -60,8 +60,8 @@
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>3.1</version>
+ <configuration>
+- <source>1.7</source>
+- <target>1.7</target>
++ <source>1.8</source>
++ <target>1.8</target>
+ </configuration>
+ </plugin>
+ <!-- Include POM.xml in source JAR -->
+@@ -141,7 +141,7 @@
+ <artifactId>maven-pmd-plugin</artifactId>
+ <version>3.1</version>
+ <configuration>
+- <targetJdk>1.7</targetJdk>
++ <targetJdk>1.8</targetJdk>
+ <linkXref>true</linkXref>
+ </configuration>
+ </plugin>
diff --git a/science/pnetcdf/Makefile b/science/pnetcdf/Makefile
index e131d647de3b..8f20c0b5240c 100644
--- a/science/pnetcdf/Makefile
+++ b/science/pnetcdf/Makefile
@@ -14,7 +14,7 @@ LICENSE_NAME= NetCDF License
LICENSE_FILE= ${WRKSRC}/COPYRIGHT
LICENSE_PERMS= auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
-USES= fortran gmake libtool mpi:${FLAVOR} pathfix perl5
+USES= fortran gmake libtool mpi:${FLAVOR} perl5
USE_PERL5= build
CFLAGS+= -fPIC
diff --git a/science/py-pyked/Makefile b/science/py-pyked/Makefile
index 44c97100f135..52b4ef9ea5f8 100644
--- a/science/py-pyked/Makefile
+++ b/science/py-pyked/Makefile
@@ -2,7 +2,7 @@ PORTNAME= pyked
DISTVERSIONPREFIX= v
DISTVERSION= 0.4.1-16
DISTVERSIONSUFFIX= -gfcccaf8
-PORTREVISION= 3
+PORTREVISION= 4
CATEGORIES= science python
#MASTER_SITES= PYPI 0.4.1 is broken there
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -15,7 +15,7 @@ LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE
RUN_DEPENDS= ${PYNUMPY} \
- ${PYTHON_PKGNAMEPREFIX}Cerberus>=1.0.0:devel/py-cerberus@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}cerberus>=1.0.0:devel/py-cerberus@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}habanero>=0.6.0:www/py-habanero@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pint>=0.7.2:devel/py-pint@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}uncertainties>=3.0.1:math/py-uncertainties@${PY_FLAVOR} \
diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile
index 26690ce9ba2e..6db6bccf7ac2 100644
--- a/science/py-qiskit/Makefile
+++ b/science/py-qiskit/Makefile
@@ -1,6 +1,6 @@
PORTNAME= qiskit
DISTVERSION= 2.2.1
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/science/tinker/Makefile b/science/tinker/Makefile
index f66cb43850b0..5f4e8fe9c739 100644
--- a/science/tinker/Makefile
+++ b/science/tinker/Makefile
@@ -1,6 +1,6 @@
PORTNAME= tinker
DISTVERSIONPREFIX= v
-DISTVERSION= 25.5.4
+DISTVERSION= 25.6.3
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/tinker/distinfo b/science/tinker/distinfo
index c80318510948..1632fdfa6948 100644
--- a/science/tinker/distinfo
+++ b/science/tinker/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1763921430
-SHA256 (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 410d02d3fe7b42b124cc38cef8cf3c077037a099465c799259f60bdae4e367b2
-SIZE (TinkerTools-tinker-v25.5.4_GH0.tar.gz) = 34197683
+TIMESTAMP = 1765785371
+SHA256 (TinkerTools-tinker-v25.6.3_GH0.tar.gz) = 83429088ba19ecd1673e53fc29c60d1787ed5c4f3ec1a4e381bfa48ab55c4af3
+SIZE (TinkerTools-tinker-v25.6.3_GH0.tar.gz) = 34581826
diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist
index cf05ef8ea37c..7d584cc522c3 100644
--- a/science/tinker/pkg-plist
+++ b/science/tinker/pkg-plist
@@ -107,8 +107,8 @@ bin/xyzpdb
%%DATADIR%%/params/water21.prm
%%DATADIR%%/params/water22.prm
%%DATADIR%%/test/0README
+%%DATADIR%%/test/anion.1st
%%DATADIR%%/test/anion.dat
-%%DATADIR%%/test/anion.dyn0
%%DATADIR%%/test/anion.key
%%DATADIR%%/test/anion.log
%%DATADIR%%/test/anion.run
@@ -219,6 +219,14 @@ bin/xyzpdb
%%DATADIR%%/test/salt.key
%%DATADIR%%/test/salt.log
%%DATADIR%%/test/salt.run
+%%DATADIR%%/test/scorpion.cif
+%%DATADIR%%/test/scorpion.key
+%%DATADIR%%/test/scorpion.log
+%%DATADIR%%/test/scorpion.run
+%%DATADIR%%/test/tip4p.key
+%%DATADIR%%/test/tip4p.log
+%%DATADIR%%/test/tip4p.run
+%%DATADIR%%/test/tip4p.xyz
%%DATADIR%%/test/vasopressin.key
%%DATADIR%%/test/vasopressin.log
%%DATADIR%%/test/vasopressin.run
generated by cgit v1.2.3 (git 2.25.1) at 2025-12-17 13:28:00 +0000