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Merge remote-tracking branch 'canonical/develop' into fix_chunk_addre…
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…ss_bugs
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@derobins
derobins committed Mar 15, 2024
2 parents a158da6 + 40e1c6d commit 89dc4b5
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10 changes: 10 additions & 0 deletions release_docs/RELEASE.txt
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Expand Up @@ -612,6 +612,13 @@ Bug Fixes since HDF5-1.14.0 release

Fixes #3003

- Fixed error when overwriting certain nested variable length types

Previously, when using a datatype that included a variable length type
within a compound or array within another variable length type, and
overwriting data with a shorter (top level) variable length sequence, an
error could occur. This has been fixed.

- Fixed asserts raised by large values of H5Pset_est_link_info() parameters

If large values for est_num_entries and/or est_name_len were passed
Expand Down Expand Up @@ -1564,6 +1571,9 @@ Known Problems
in the HDF5 source. Please report any new problems found to
[email protected].

File space may not be released when overwriting or deleting certain nested
variable length or reference types.


CMake vs. Autotools installations
=================================
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2 changes: 0 additions & 2 deletions src/H5A.c
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Expand Up @@ -25,9 +25,7 @@
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5ESprivate.h" /* Event Sets */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Opkg.h" /* Object headers */
#include "H5Sprivate.h" /* Dataspace functions */
#include "H5VLprivate.h" /* Virtual Object Layer */
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1 change: 0 additions & 1 deletion src/H5AC.c
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Expand Up @@ -40,7 +40,6 @@
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* Files */
#include "H5Iprivate.h" /* IDs */
#include "H5Pprivate.h" /* Property lists */
#include "H5SLprivate.h" /* Skip Lists */

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1 change: 0 additions & 1 deletion src/H5Adeprec.c
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Expand Up @@ -35,7 +35,6 @@
#include "H5private.h" /* Generic Functions */
#include "H5Apkg.h" /* Attributes */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dprivate.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
#include "H5Opkg.h" /* Object headers */
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2 changes: 0 additions & 2 deletions src/H5Aint.c
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Expand Up @@ -31,8 +31,6 @@
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Apkg.h" /* Attributes */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dprivate.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
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1 change: 0 additions & 1 deletion src/H5Atest.c
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Expand Up @@ -31,7 +31,6 @@
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Apkg.h" /* Attributes */
#include "H5ACprivate.h" /* Metadata cache */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
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2 changes: 0 additions & 2 deletions src/H5B.c
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Expand Up @@ -101,10 +101,8 @@
#include "H5Bpkg.h" /* B-link trees */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Pprivate.h" /* Property lists */

/****************/
/* Local Macros */
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7 changes: 3 additions & 4 deletions src/H5B2dbg.c
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Expand Up @@ -28,10 +28,9 @@
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5B2pkg.h" /* v2 B-trees */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5private.h" /* Generic Functions */
#include "H5B2pkg.h" /* v2 B-trees */
#include "H5Eprivate.h" /* Error handling */

/****************/
/* Local Macros */
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6 changes: 3 additions & 3 deletions src/H5CX.c
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Expand Up @@ -300,9 +300,9 @@ typedef struct H5CX_t {
bool no_selection_io_cause_valid; /* Whether reason for not performing selection I/O is valid */

uint32_t
actual_selection_io_mode; /* Actual selection I/O mode used (H5D_ACTUAL_SELECTION_IO_MODE_NAME) */
hbool_t actual_selection_io_mode_set; /* Whether actual selection I/O mode is set */
hbool_t actual_selection_io_mode_valid; /* Whether actual selection I/O mode is valid */
actual_selection_io_mode; /* Actual selection I/O mode used (H5D_ACTUAL_SELECTION_IO_MODE_NAME) */
bool actual_selection_io_mode_set; /* Whether actual selection I/O mode is set */
bool actual_selection_io_mode_valid; /* Whether actual selection I/O mode is valid */

/* Cached LCPL properties */
H5T_cset_t encoding; /* Link name character encoding */
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1 change: 0 additions & 1 deletion src/H5Cimage.c
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Expand Up @@ -40,7 +40,6 @@
#include "H5Fpkg.h" /* Files */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */

/****************/
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1 change: 0 additions & 1 deletion src/H5Ctag.c
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Expand Up @@ -37,7 +37,6 @@
#include "H5Eprivate.h" /* Error Handling */
#include "H5Fpkg.h" /* Files */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MMprivate.h" /* Memory management */

/****************/
/* Local Macros */
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1 change: 0 additions & 1 deletion src/H5Dbtree.c
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Expand Up @@ -31,7 +31,6 @@
#include "H5Fprivate.h" /* Files */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File space management */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
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2 changes: 0 additions & 2 deletions src/H5Dcontig.c
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Expand Up @@ -36,9 +36,7 @@
#include "H5Iprivate.h" /* IDs */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5FOprivate.h" /* File objects */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
#include "H5PBprivate.h" /* Page Buffer */
#include "H5VMprivate.h" /* Vector and array functions */

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1 change: 0 additions & 1 deletion src/H5Ddbg.c
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Expand Up @@ -20,7 +20,6 @@
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Iprivate.h" /* IDs */
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2 changes: 0 additions & 2 deletions src/H5Dfill.c
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Expand Up @@ -29,11 +29,9 @@
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector and array functions */
#include "H5WBprivate.h" /* Wrapped Buffers */
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3 changes: 0 additions & 3 deletions src/H5Dio.c
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Expand Up @@ -24,12 +24,9 @@
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Sprivate.h" /* Dataspace */

#include "H5VLnative_private.h" /* Native VOL connector */

/****************/
/* Local Macros */
/****************/
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1 change: 0 additions & 1 deletion src/H5Dmpio.c
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Expand Up @@ -30,7 +30,6 @@
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
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1 change: 0 additions & 1 deletion src/H5Dnone.c
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Expand Up @@ -34,7 +34,6 @@
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MFprivate.h" /* File space management */
#include "H5VMprivate.h" /* Vector functions */

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1 change: 0 additions & 1 deletion src/H5Dscatgath.c
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Expand Up @@ -24,7 +24,6 @@
#include "H5Dpkg.h" /* Dataset functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */

/****************/
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2 changes: 0 additions & 2 deletions src/H5Dsingle.c
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Expand Up @@ -30,9 +30,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MFprivate.h" /* File space management */
#include "H5VMprivate.h" /* Vector functions */

/****************/
/* Local Macros */
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3 changes: 0 additions & 3 deletions src/H5EAcache.c
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Expand Up @@ -35,10 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
#include "H5WBprivate.h" /* Wrapped Buffers */

/****************/
/* Local Macros */
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1 change: 0 additions & 1 deletion src/H5EAdblkpage.c
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Expand Up @@ -36,7 +36,6 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5EApkg.h" /* Extensible Arrays */
#include "H5FLprivate.h" /* Free Lists */
#include "H5VMprivate.h" /* Vectors and arrays */

/****************/
/* Local Macros */
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1 change: 1 addition & 0 deletions src/H5EApkg.h
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Expand Up @@ -27,6 +27,7 @@

/* Other private headers needed by this file */
#include "H5FLprivate.h" /* Free Lists */
#include "H5VMprivate.h" /* Vectors and arrays */

/**************************/
/* Package Private Macros */
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1 change: 0 additions & 1 deletion src/H5ES.c
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Expand Up @@ -35,7 +35,6 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5ESpkg.h" /* Event Sets */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */

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7 changes: 3 additions & 4 deletions src/H5ESlist.c
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Expand Up @@ -32,10 +32,9 @@
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5ESpkg.h" /* Event Sets */
#include "H5FLprivate.h" /* Free Lists */
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5ESpkg.h" /* Event Sets */

/****************/
/* Local Macros */
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3 changes: 0 additions & 3 deletions src/H5FAcache.c
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Expand Up @@ -35,10 +35,7 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FApkg.h" /* Fixed Arrays */
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
#include "H5WBprivate.h" /* Wrapped Buffers */

/****************/
/* Local Macros */
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1 change: 0 additions & 1 deletion src/H5FAdbg.c
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Expand Up @@ -35,7 +35,6 @@
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FApkg.h" /* Fixed Arrays */
#include "H5Oprivate.h" /* Object Header */
#include "H5VMprivate.h" /* Vector functions */

/****************/
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1 change: 0 additions & 1 deletion src/H5FD.c
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Expand Up @@ -30,7 +30,6 @@
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dprivate.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* File access */
#include "H5FDpkg.h" /* File Drivers */
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1 change: 0 additions & 1 deletion src/H5FDfamily.c
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Expand Up @@ -31,7 +31,6 @@
#include "H5FDdrvr_module.h" /* This source code file is part of the H5FD driver module */

#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
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6 changes: 3 additions & 3 deletions src/H5FDint.c
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Expand Up @@ -376,7 +376,7 @@ H5FD_read_vector(H5FD_t *file, uint32_t count, H5FD_mem_t types[], haddr_t addrs
size_t size = 0;
H5FD_mem_t type = H5FD_MEM_DEFAULT;
hid_t dxpl_id = H5I_INVALID_HID; /* DXPL for operation */
hbool_t is_raw = FALSE; /* Does this include raw data */
bool is_raw = false; /* Does this include raw data */
herr_t ret_value = SUCCEED; /* Return value */

FUNC_ENTER_NOAPI(FAIL)
Expand Down Expand Up @@ -461,7 +461,7 @@ H5FD_read_vector(H5FD_t *file, uint32_t count, H5FD_mem_t types[], haddr_t addrs

/* Check for raw data operation */
if (type == H5FD_MEM_DRAW)
is_raw = TRUE;
is_raw = true;
}
}

Expand Down Expand Up @@ -618,7 +618,7 @@ H5FD_write_vector(H5FD_t *file, uint32_t count, H5FD_mem_t types[], haddr_t addr
H5FD_mem_t type = H5FD_MEM_DEFAULT;
hid_t dxpl_id; /* DXPL for operation */
haddr_t eoa = HADDR_UNDEF; /* EOA for file */
hbool_t is_raw = FALSE; /* Does this include raw data */
bool is_raw = false; /* Does this include raw data */
herr_t ret_value = SUCCEED; /* Return value */

FUNC_ENTER_NOAPI(FAIL)
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3 changes: 0 additions & 3 deletions src/H5FDmpi.c
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Expand Up @@ -15,12 +15,9 @@
*/

#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5FDmpi.h" /* Common MPI file driver */
#include "H5Pprivate.h" /* Property lists */

#ifdef H5_HAVE_PARALLEL

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2 changes: 1 addition & 1 deletion src/H5FDmpio.c
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Expand Up @@ -38,7 +38,7 @@ static hid_t H5FD_MPIO_g = 0;

/* Whether to allow collective I/O operations */
/* (Can be changed by setting "HDF5_MPI_OPT_TYPES" environment variable to '0' or '1') */
hbool_t H5FD_mpi_opt_types_g = true;
bool H5FD_mpi_opt_types_g = true;

/* Whether the driver initialized MPI on its own */
static bool H5FD_mpi_self_initialized = false;
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9 changes: 4 additions & 5 deletions src/H5FDperform.c
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Expand Up @@ -19,11 +19,10 @@
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Eprivate.h" /* Error handling */
#include "H5FDpkg.h" /* File Drivers */
#include "H5Iprivate.h" /* IDs */
#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5FDpkg.h" /* File Drivers */
#include "H5Iprivate.h" /* IDs */

/*-------------------------------------------------------------------------
* Function: H5FDperform_init
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1 change: 0 additions & 1 deletion src/H5FDsec2.c
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Expand Up @@ -28,7 +28,6 @@
#include "H5FDsec2.h" /* Sec2 file driver */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Pprivate.h" /* Property lists */

/* The driver identification number, initialized at runtime */
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4 changes: 0 additions & 4 deletions src/H5FDwindows.c
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Expand Up @@ -12,13 +12,9 @@

#include "H5private.h" /* Generic Functions */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5FDwindows.h" /* Windows file driver */
#include "H5FDsec2.h" /* Windows file driver */
#include "H5FLprivate.h" /* Free Lists */
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Pprivate.h" /* Property lists */

#ifdef H5_HAVE_WINDOWS
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1 change: 0 additions & 1 deletion src/H5FScache.c
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Expand Up @@ -36,7 +36,6 @@
#include "H5MFprivate.h" /* File memory management */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vectors and arrays */
#include "H5WBprivate.h" /* Wrapped Buffers */

/****************/
/* Local Macros */
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1 change: 0 additions & 1 deletion src/H5Fdeprec.c
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Expand Up @@ -36,7 +36,6 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Fpkg.h" /* File access */
#include "H5Iprivate.h" /* IDs */
#include "H5SMprivate.h" /* Shared object header messages */

#include "H5VLnative_private.h" /* Native VOL connector */

Expand Down
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