Date: Mon, 18 Jul 2022 12:51:52 GMT From: Po-Chuan Hsieh <sunpoet@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: ba66c05b01ae - main - biology/sra-tools: Fix build with HDF5 1.12.0+ Message-ID: <202207181251.26ICpqVP091972@gitrepo.freebsd.org>
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The branch main has been updated by sunpoet: URL: https://cgit.FreeBSD.org/ports/commit/?id=ba66c05b01aeb7d0000c13193536d283e6e55077 commit ba66c05b01aeb7d0000c13193536d283e6e55077 Author: Po-Chuan Hsieh <sunpoet@FreeBSD.org> AuthorDate: 2022-07-18 12:50:17 +0000 Commit: Po-Chuan Hsieh <sunpoet@FreeBSD.org> CommitDate: 2022-07-18 12:50:17 +0000 biology/sra-tools: Fix build with HDF5 1.12.0+ --- biology/sra-tools/files/patch-hdf5 | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/biology/sra-tools/files/patch-hdf5 b/biology/sra-tools/files/patch-hdf5 new file mode 100644 index 000000000000..a99f56d25e46 --- /dev/null +++ b/biology/sra-tools/files/patch-hdf5 @@ -0,0 +1,30 @@ +--- ncbi-vdb/interfaces/ext/hdf5/H5Opublic.h.orig 2021-03-15 18:16:43 UTC ++++ ncbi-vdb/interfaces/ext/hdf5/H5Opublic.h +@@ -150,8 +150,13 @@ H5_DLL hid_t H5Oopen_by_idx(hid_t loc_id, const char * + H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t lapl_id); + H5_DLL htri_t H5Oexists_by_name(hid_t loc_id, const char *name, hid_t lapl_id); + H5_DLL herr_t H5Oget_info(hid_t loc_id, H5O_info_t *oinfo); ++#if H5_VERSION_GE(1,12,0) ++H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo, unsigned fields, ++ hid_t lapl_id); ++#else + H5_DLL herr_t H5Oget_info_by_name(hid_t loc_id, const char *name, H5O_info_t *oinfo, + hid_t lapl_id); ++#endif + H5_DLL herr_t H5Oget_info_by_idx(hid_t loc_id, const char *group_name, + H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5O_info_t *oinfo, + hid_t lapl_id); +--- ncbi-vdb/libs/hdf5/hdf5dir.c.orig 2021-03-15 18:16:43 UTC ++++ ncbi-vdb/libs/hdf5/hdf5dir.c +@@ -292,7 +292,11 @@ rc_t CC HDF5DirVisitUpdate ( HDF5Dir *self, bool recur + static uint32_t HDF5DirPathTypeOnBuffer( const HDF5Dir *self, const char *buffer ) + { + H5O_info_t obj_info; ++#if H5_VERSION_GE(1,12,0) ++ herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5O_INFO_BASIC, H5P_DEFAULT ); ++#else + herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5P_DEFAULT ); ++#endif + if ( h5e >= 0 ) + { + switch( obj_info.type )
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