Date: Sun, 23 Nov 2025 20:09:17 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: f04154321aa1 - main - science/silo: update 4.11=?utf-8?Q?-68 =E2=86=92?= 4.12.0 Message-ID: <692369ed.2c832.38831ab3@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=f04154321aa10deb15b9f712159e08a52c29f30b commit f04154321aa10deb15b9f712159e08a52c29f30b Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2025-11-23 19:10:23 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2025-11-23 20:09:01 +0000 science/silo: update 4.11-68 → 4.12.0 Reported by: portscout --- misc/lbann/Makefile | 2 +- science/ascent/Makefile | 1 + science/axom/Makefile | 2 +- science/conduit/Makefile | 1 + science/parthenon/Makefile | 2 +- science/polytope/Makefile | 1 + science/serac/Makefile | 2 +- science/silo/Makefile | 5 +-- science/silo/distinfo | 6 +-- science/silo/files/patch-CMakeLists.txt | 13 +++++++ science/silo/files/patch-git-commit-be29ddf | 44 ---------------------- science/silo/files/patch-src_silo_silo.c | 39 ------------------- science/silo/files/patch-src_silo_silo__json.c | 4 +- .../patch-tests_CMake_SiloMakeCheckRunner.cmake | 13 ------- science/silo/pkg-plist | 13 ++++--- science/spheral/Makefile | 2 +- 16 files changed, 35 insertions(+), 115 deletions(-) diff --git a/misc/lbann/Makefile b/misc/lbann/Makefile index be4656410487..2767e9e0adef 100644 --- a/misc/lbann/Makefile +++ b/misc/lbann/Makefile @@ -2,7 +2,7 @@ PORTNAME= lbann DISTVERSIONPREFIX= v DISTVERSION= 0.102-254 DISTVERSIONSUFFIX= -g2e3012a9a -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= misc # machine-learning MAINTAINER= yuri@FreeBSD.org diff --git a/science/ascent/Makefile b/science/ascent/Makefile index 700c3175eeba..1687ea96d527 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,6 +1,7 @@ PORTNAME= ascent DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -visualizer diff --git a/science/axom/Makefile b/science/axom/Makefile index 25a79bc28304..254bf8397995 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,7 +1,7 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/conduit/Makefile b/science/conduit/Makefile index fe04ba696b7a..5f2c3994456b 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,6 +1,7 @@ PORTNAME= conduit DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/parthenon/Makefile b/science/parthenon/Makefile index 98f08b45d7b7..b09ecf9ad2ee 100644 --- a/science/parthenon/Makefile +++ b/science/parthenon/Makefile @@ -1,7 +1,7 @@ PORTNAME= parthenon DISTVERSIONPREFIX= v DISTVERSION= 24.08 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/polytope/Makefile b/science/polytope/Makefile index cd2985964500..51d29d283c38 100644 --- a/science/polytope/Makefile +++ b/science/polytope/Makefile @@ -1,5 +1,6 @@ PORTNAME= polytope DISTVERSION= 0.7.4 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/serac/Makefile b/science/serac/Makefile index 79535619d3e5..9ced914a7e86 100644 --- a/science/serac/Makefile +++ b/science/serac/Makefile @@ -1,6 +1,6 @@ PORTNAME= serac PORTVERSION= g20220823 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org diff --git a/science/silo/Makefile b/science/silo/Makefile index 9759d1b7565c..dac1c6649952 100644 --- a/science/silo/Makefile +++ b/science/silo/Makefile @@ -1,7 +1,5 @@ PORTNAME= silo -DISTVERSION= 4.11-68 -PORTREVISION= 1 -DISTVERSIONSUFFIX= -g819658e +DISTVERSION= 4.12.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -19,6 +17,7 @@ USE_GITHUB= yes GH_ACCOUNT= LLNL GH_PROJECT= Silo +CMAKE_ON= SILO_ENABLE_INSTALL_LITE_HEADERS CMAKE_TESTING_ON= SILO_ENABLE_TESTS # 3 tests fail, see https://github.com/LLNL/Silo/issues/289 CMAKE_TESTING_TARGET= check diff --git a/science/silo/distinfo b/science/silo/distinfo index a3cf26715bd2..2fe4efe79810 100644 --- a/science/silo/distinfo +++ b/science/silo/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1670041617 -SHA256 (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 3a7a75e196c9e39922998054378efa02b2d24dc57ab126ab15a631e2645bd0ce -SIZE (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 14028123 +TIMESTAMP = 1763923185 +SHA256 (LLNL-Silo-4.12.0_GH0.tar.gz) = 5251816e43b08c19c925480b2daf85cc9b75e494b91df37df0eacc092279cfd0 +SIZE (LLNL-Silo-4.12.0_GH0.tar.gz) = 99198889 diff --git a/science/silo/files/patch-CMakeLists.txt b/science/silo/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..1d76b4832b67 --- /dev/null +++ b/science/silo/files/patch-CMakeLists.txt @@ -0,0 +1,13 @@ +- workaround for https://github.com/LLNL/Silo/issues/501 + +--- CMakeLists.txt.orig 2025-11-23 19:03:43 UTC ++++ CMakeLists.txt +@@ -700,7 +700,7 @@ install(FILES ${silo_public_headers} DESTINATION ${CMA + WORLD_READ) + + # Symlink old style silo_f77.inc +-if(SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) ++if(FALSE AND SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER) + install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink silo.inc silo_f77.inc + WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})") + endif() diff --git a/science/silo/files/patch-git-commit-be29ddf b/science/silo/files/patch-git-commit-be29ddf deleted file mode 100644 index fba494b0b956..000000000000 --- a/science/silo/files/patch-git-commit-be29ddf +++ /dev/null @@ -1,44 +0,0 @@ -commit be29ddf0352bc8e5a7eecc8772a3acb64dfde18c -Author: miller86 <miller86@llnl.gov> -Date: Fri Dec 2 19:00:20 2022 -0800 - - fix obj-case-macro - -diff --git src/hdf5_drv/silo_hdf5.c src/hdf5_drv/silo_hdf5.c -index 17af250..c45d689 100644 ---- src/hdf5_drv/silo_hdf5.c -+++ src/hdf5_drv/silo_hdf5.c -@@ -1809,7 +1809,7 @@ db_hdf5_cwg(DBfile *_dbfile) - *dscount = m.MEMCNT; \ - *dsnames = (char **) calloc(*dscount, sizeof(char**)); \ - for (i = 0; i < *dscount; i++) \ -- (*dsnames)[i] = strdup(m.MEMNAME[i]); \ -+ (*dsnames)[i] = strdup(m.MEMNAME); \ - break; \ - } - -@@ -1857,15 +1857,15 @@ db_hdf5_get_obj_dsnames(DBfile *_dbfile, char const *name, int *dscount, char ** - - switch(_objtype) - { -- DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value) -- /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord) wont work for rect case */ -- DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord) -- DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value) -- DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data) -- DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord) -- DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals) -+ DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value[i]) -+ /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord[i]) wont work for rect case */ -+ DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord[i]) -+ DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value[i]) -+ DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data[i]) -+ DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord[i]) -+ DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals[i]) - DB_OBJ_CASE(DB_CURVE, DBcurve_mt, npts?1:1, yvarname) - } - H5Tclose(o); diff --git a/science/silo/files/patch-src_silo_silo.c b/science/silo/files/patch-src_silo_silo.c deleted file mode 100644 index d20855c5ca9b..000000000000 --- a/science/silo/files/patch-src_silo_silo.c +++ /dev/null @@ -1,39 +0,0 @@ ---- src/silo/silo.c.orig 2022-12-03 02:30:10 UTC -+++ src/silo/silo.c -@@ -238,12 +238,8 @@ typedef struct db_silo_stat_t { - #ifndef SIZEOF_OFF64_T - #error missing definition for SIZEOF_OFF64_T in silo_private.h - #else --#if SIZEOF_OFF64_T > 4 -- struct stat64 s; --#else - struct stat s; - #endif --#endif - #ifdef _WIN32 - DWORD fileindexlo; - DWORD fileindexhi; -@@ -2121,11 +2117,7 @@ db_silo_stat_one_file(const char *name, db_silo_stat_t - errno = 0; - memset(&(statbuf->s), 0, sizeof(statbuf->s)); - --#if SIZEOF_OFF64_T > 4 -- retval = stat64(name, &(statbuf->s)); --#else - retval = stat(name, &(statbuf->s)); --#endif /* #if SIZEOF_OFF64_T > 4 */ - - #ifdef _WIN32 - if (retval == 0) -@@ -4136,11 +4128,7 @@ DBOpenReal(const char *name, int type, int mode) - /********************************/ - /* System level error occured. */ - /********************************/ --#if SIZEOF_OFF64_T > 4 -- printf("stat64() failed with error: "); --#else - printf("stat() failed with error: "); --#endif - switch (errno) - { - case EACCES: printf("EACCES\n"); break; diff --git a/science/silo/files/patch-src_silo_silo__json.c b/science/silo/files/patch-src_silo_silo__json.c index 576f7eea757f..331a87c8890e 100644 --- a/science/silo/files/patch-src_silo_silo__json.c +++ b/science/silo/files/patch-src_silo_silo__json.c @@ -1,6 +1,6 @@ ---- src/silo/silo_json.c.orig 2022-12-03 02:30:10 UTC +--- src/silo/silo_json.c.orig 2025-11-21 05:30:59 UTC +++ src/silo/silo_json.c -@@ -441,11 +441,7 @@ json_object_from_binary_file(char const *filename) +@@ -446,11 +446,7 @@ json_object_from_binary_file(char const *filename) #ifndef SIZEOF_OFF64_T #error missing definition for SIZEOF_OFF64_T in silo_private.h #else diff --git a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake b/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake deleted file mode 100644 index c25272a9a103..000000000000 --- a/science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake +++ /dev/null @@ -1,13 +0,0 @@ -- workaround for https://github.com/LLNL/Silo/issues/288 - ---- tests/CMake/SiloMakeCheckRunner.cmake.orig 2022-12-03 06:53:38 UTC -+++ tests/CMake/SiloMakeCheckRunner.cmake -@@ -72,7 +72,7 @@ function(silo_add_make_check_runner) - message(WARNING "silo_add_make_check_runner: NAME argument is required.") - return() - endif() -- set(test_cmd ${samcr_NAME}) -+ set(test_cmd "./${samcr_NAME}") - if("ARGS" IN_LIST samcr_KEYWORDS_MISSING_VALUES) - message(WARNING "silo_add_make_check_runner: ARGS argument provided without a value.") - return() diff --git a/science/silo/pkg-plist b/science/silo/pkg-plist index c55c7a873580..fc056e66313d 100644 --- a/science/silo/pkg-plist +++ b/science/silo/pkg-plist @@ -3,18 +3,19 @@ %%SILOCK%%bin/silock %%BROWSER%%bin/silodiff %%BROWSER%%bin/silofile -cmake/SiloConfig.cmake -cmake/SiloConfigVersion.cmake -cmake/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake -cmake/SiloTargets.cmake include/lite_pdb.h include/lite_score.h -include/pdform.h include/pmpio.h include/silo.h -include/silo.inc +%%FORTRAN%%include/silo.inc %%FORTRAN%%include/silo_FC.h include/silo_exports.h include/silo_f9x.inc %%PYTHON%%lib/Silo.so +lib/cmake/Silo/SiloConfig.cmake +lib/cmake/Silo/SiloConfigVersion.cmake +lib/cmake/Silo/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Silo/SiloTargets.cmake lib/libsilo%%SUFX_HDF5%%.so +lib/libsilo%%SUFX_HDF5%%.so.4.12.0 +lib/libsilo%%SUFX_HDF5%%.so.412 diff --git a/science/spheral/Makefile b/science/spheral/Makefile index 1f6d29f4af1c..d35d06393bf2 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,7 +1,7 @@ PORTNAME= spheral DISTVERSIONPREFIX= v DISTVERSION= 2025.06.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.orghome | help
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