30: H5close <- function( ) {

93: .H5close <- function(h5id){

102:     closeFunc <- switch(truetype,

84: h5closeAll <- function(...) {

7: #' * `H5close` flushes all data to disk, closes all open identifiers, and cleans up memory.

15: #'   H5close()

31:   invisible(.Call("_H5close", PACKAGE='rhdf5'))

46: #' Close open HDF5 handles

49: #' more [H5IdComponent-class] objects and it'll will try to close all of them

55: #' getting to the close statement, or the open handle was not assigned to an R

79: #' ## close all open identifiers and verify

90:     invisible(lapply(objects, .H5close))

109:                         stop("Error in h5closeAll(). Appropriate close function not found", call. = FALSE)

51: #' can be easier than making multiple calls to [H5Fclose()], [H5Gclose()], etc.

54: #' created and not closed correctly.  Maybe because a function stopped before

57: #' handles and closes them.

60: #'   closed.  If nothing is provided to the function, all open handles will be

61: #'   closed.

72: #' h5File <- tempfile(pattern = "ex_h5closeAll.h5")

80: #' h5closeAll()

83: #' @export h5closeAll

97:         stop("Error in h5closeAll(). H5Identifier not valid.", call. = FALSE)

103:                         H5I_FILE = H5Fclose,

104:                         H5I_GROUP = H5Gclose,

105:                         H5I_DATASET = H5Dclose,

106:                         H5I_GENPROP_LST = H5Pclose,

107:                         H5I_DATASPACE = H5Sclose,

108:                         H5I_ATTR = H5Aclose,

112:     closeFunc(h5id)

20: SEXP _H5close(void) {

4: SEXP _H5close(void);

19: /* herr_t H5close(void) */

21:   herr_t herr = H5close();

73: H5Pclose <- function( h5plist ) {

785: H5Pclose_class <- function( h5plistclass ) {

62: #' Close and release a property list

70: #' to close.

64: #' `H5Pclose()` terminates access to a property list. All property lists 

65: #' should be closed when they no longer need to be accessed. This 

66: #' frees resources used by the property list.  Failing to call `H5Pclose()`

75:   invisible(.Call("_H5Pclose", h5plist@ID, PACKAGE='rhdf5'))

262: #' H5Pclose(pid)

357: #' H5Pclose(pid)

787:   invisible(.Call("_H5Pclose_class", h5plistclass@ID, PACKAGE='rhdf5'))

45: SEXP _H5Pclose( SEXP _plist ) {

2051: SEXP _H5Pclose_class( SEXP _class ) {

280: /* /\* /\\* herr_t H5Pset_fclose_degree(hid_t fapl_id, H5F_close_degree_t fc_degree) *\\/ *\/ */

283: /* /\*   TODO: H5F_close_degree_t fc_degree = _fc_degree *\/ */

284: /* /\*   herr_t herr = H5Pset_fclose_degree(hid_tfapl_id, H5F_close_degree_tfc_degree); *\/ */

289: /* /\* herr_t H5Pget_fclose_degree(hid_t fapl_id, H5F_close_degree_t * fc_degree) *\/ */

292: /*   TODO: H5F_close_degree_t * fc_degree = _fc_degree */

293: /*   herr_t herr = H5Pget_fclose_degree(hid_tfapl_id, H5F_close_degree_t *fc_degree); */

1843: ...(70 bytes skipped)...P_cls_create_func_t create, void * create_data, H5P_cls_copy_func_t copy, void * copy_data, H5P_cls_close_func_t close, void * close_data) *\/ */

1844: ...(26 bytes skipped)...SEXP _parent_class, SEXP _name, SEXP _create, SEXP _create_data, SEXP _copy, SEXP _copy_data, SEXP _close, SEXP _close_data ) { */

1851: /*   TODO: H5P_cls_close_func_t close = _close */

1852: /*   TODO: void * close_data = _close_data */

1853: ...(68 bytes skipped)..., H5P_cls_create_func_tcreate, void *create_data, H5P_cls_copy_func_tcopy, void *copy_data, H5P_cls_close_func_tclose, void *close_data); */

1859: ...(130 bytes skipped)...func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_close_func_t close) *\/ */

1860: ...(43 bytes skipped)...ame, SEXP _size, SEXP _default, SEXP _create, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _close ) { */

1870: /*   TODO: H5P_prp_close_func_t close = _close */

1871: ...(126 bytes skipped)...set_func_tset, H5P_prp_get_func_tget, H5P_prp_delete_func_tdelete, H5P_prp_copy_func_tcopy, H5P_prp_close_func_tclose); */

1876: ...(162 bytes skipped)...et, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close) *\/ */

1877: ...(58 bytes skipped)..., SEXP _default, SEXP _create, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _compare, SEXP _close ) { */

1888: /*   TODO: H5P_prp_close_func_t close = _close */

1889: ...(157 bytes skipped)..._tget, H5P_prp_delete_func_tdelete, H5P_prp_copy_func_tcopy, H5P_prp_compare_func_tcompare, H5P_prp_close_func_tclose); */

1894: ...(95 bytes skipped)...func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_close_func_t close) *\/ */

1895: ...(24 bytes skipped)...P _plid, SEXP _name, SEXP _size, SEXP _value, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _close ) { */

1904: /*   TODO: H5P_prp_close_func_t close = _close */

1905: ...(92 bytes skipped)...set_func_tset, H5P_prp_get_func_tget, H5P_prp_delete_func_tdelete, H5P_prp_copy_func_tcopy, H5P_prp_close_func_tclose); */

1910: ...(127 bytes skipped)...et, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close) *\/ */

1911: ...(39 bytes skipped)...name, SEXP _size, SEXP _value, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _compare, SEXP _close ) { */

1921: /*   TODO: H5P_prp_close_func_t close = _close */

1922: ...(123 bytes skipped)..._tget, H5P_prp_delete_func_tdelete, H5P_prp_copy_func_tcopy, H5P_prp_compare_func_tcompare, H5P_prp_close_func_tclose); */

44: /* herr_t H5Pclose(hid_t plist ) */

47:     herr_t herr = H5Pclose( plist );

281: /* /\* SEXP _H5Pset_fclose_degree( SEXP _fapl_id, SEXP _fc_degree ) { *\/ */

290: /* SEXP _H5Pget_fclose_degree( SEXP _fapl_id, SEXP _fc_degree ) { */

2050: /* herr_t H5Pclose_class( hid_t class ) */

2053:     herr_t herr = H5Pclose_class( class );

77: H5Sclose <- function( h5space ) {

69: #' Close and release a dataspace

72: #' dataspace to be closed.

79:   invisible(.Call("_H5Sclose", h5space@ID, PACKAGE='rhdf5'))

281: #' H5Sclose(sid_1)

377: #' H5Sclose(sid_1)

378: #' H5Sclose(sid_2)

486: #' H5Sclose(sid_1)

487: #' H5Sclose(sid_2)

488: #' H5Sclose(sid_3)

85: H5Dclose <- function( h5dataset ) {

60: #' ## rember to close open handles

79: #' Close an open HDF5 dataset

48: #' To prevent memory leaks this must be closed with a call to [H5Dclose()] 

61: #' H5Dclose( did )

62: #' H5Fclose( fid )

87:   invisible(.Call("_H5Dclose", h5dataset@ID, PACKAGE='rhdf5'))

167:     on.exit(H5Aclose(att))

130: H5Aclose <- function( h5attribute ) {

123: #' Close an HDF5 attribute

126: #' the attribute to be closed.  Normally created by [H5Aopen()] or similar.

132:   invisible(.Call("_H5Aclose", h5attribute@ID, PACKAGE='rhdf5'))

97: SEXP _H5Dclose( SEXP _dataset_id ) {

927:     // close data type

930:     // close mem space

938:     // close file space 

96: /* herr_t H5Dclose(hid_t dataset_id ) */

100:     herr_t herr = H5Dclose( dataset_id );

821:     herr = H5Tclose(dtype_id);

928:     H5Tclose(dtype_id);

932:         H5Sclose(mem_space_id);

940:         H5Sclose(file_space_id);

97: H5Fclose <- function( h5file ) {

91: #' Close access to an HDF5 file

30:         ## create a new property list, and make sure it is closed

32:         on.exit(H5Pclose(fapl))

76:     on.exit(H5Pclose(fapl))

99:   invisible(.Call("_H5Fclose", h5file@ID, PACKAGE='rhdf5'))

219: #' H5Dclose(did)

220: #' H5Gclose(gid)

221: #' H5Fclose(fid)

79: SEXP _H5Aclose( SEXP _attr_id ) {

414:   // close mem space

420:   // close file space

78: /* herr_t H5Aclose(hid_t attr_id) */

81:   herr_t herr = H5Aclose( attr_id );

415:   H5Sclose(mem_space_id);

421:   H5Sclose(file_space_id);

28: SEXP _H5Sclose( SEXP _space_id ) {

27: /* herr_t H5Sclose( hid_t space_id ) */

30:     herr_t herr = H5Sclose( space_id );

79: H5Gclose <- function( h5group ) {

73: #' Close a specified group

31: #' is closed.

55: #' with [H5Gclose()] to prevent resource leakage.

57: #' @seealso [H5Gclose()]

81:   invisible(.Call("_H5Gclose", h5group@ID, PACKAGE='rhdf5'))

103: #' H5Gclose(gid)

110: #' H5Fclose(fid)

52: SEXP _H5Fclose( SEXP _file_id ) {

51: /* herr_t H5Fclose( hid_t file_id ) */

54:   herr_t herr = H5Fclose( file_id );

51: H5Oclose <- function( h5obj ) {

43: #' Close an HDF5 object

24: #' H5Oclose(oid)

25: #' H5Fclose(fid)

27: #' @seealso [H5Oclose()]

53:   invisible(.Call("_H5Oclose", h5obj@ID, PACKAGE='rhdf5'))

94: #' H5Pclose(lcpl)

95: #' H5Fclose(fid1)

96: #' H5Fclose(fid2)

111:     on.exit(H5Pclose(lcpl), add = TRUE)

119:     on.exit(H5Pclose(obj_cpy_pl), add = TRUE)

160: #' H5Gclose(gid)

161: #' H5Fclose(fid)

68: SEXP _H5Oclose( SEXP _object_id ) {

70:   herr_t herr = H5Oclose( object_id );

151:     //  H5Oclose(oid);

158:     H5Fclose(loc_id);

48: SEXP _H5Gclose( SEXP _group_id ) {

47: /* herr_t H5Gclose(hid_t group_id) */

51:   herr_t herr = H5Gclose( group_id );

218: static void bsClose ( BitStream* bs )

233:    retVal = fclose ( bs->handle );

413:    bsClose ( bsIn );

460:             bsClose ( bsWr );

170: h5closeitLoc <- function(file, fctname = deparse(match.call()[1])) {

212: h5closeitObj <- function(obj, fctname = deparse(match.call()[1])) {

113:         "Run 'h5closeAll()' to close all open HDF5 object handles.")

123:         res$closeit = TRUE

132:           res$closeit = TRUE

139:     ## We have passed an H5IdComponent, so it should not be closed after  

142:     res$closeit = FALSE

158:       res$closeit = TRUE

162:   ## We have passed an H5IdComponent, so it should not be closed after  

165:     res$closeit = FALSE

172:   if (file$closeit) {

174:       res = H5Fclose(file$H5Identifier)

200:         res$closeit = TRUE

203:     h5closeitLoc(loc)   

207:     res$closeit = FALSE

214:   if (obj$closeit) {

216:       res = H5Oclose(obj$H5Identifier)

252:     H5Pclose_class(h5plc)

940: static size_t HUF_closeCStream(HUF_CStream_t* bitC)

415:                 /* only triggered when no more rank 1 symbol left => find closest one (note : there is necessarily at least one !) */

937: /*! HUF_closeCStream() :

1084:     return HUF_closeCStream(&bitC);

234: MEM_STATIC size_t BIT_closeCStream(BIT_CStream_t* bitC)

84: *  Last operation is to close the bitStream.

70: MEM_STATIC size_t BIT_closeCStream(BIT_CStream_t* bitC);

218:  *  overflow will be revealed later on using BIT_closeCStream() */

231: /*! BIT_closeCStream() :

2023: static int ZSTD_indexTooCloseToMax(ZSTD_window_t w)

2086:         int const indexTooClose = ZSTD_indexTooCloseToMax(zc->blockState.matchState.window);

2089:             (indexTooClose || dictTooBig || !zc->initialized) ? ZSTDirp_reset : ZSTDirp_continue;

2015: /* ZSTD_indexTooCloseToMax() :

5: \title{Close an open HDF5 dataset}

14: Close an open HDF5 dataset

3: \name{H5Dclose}

4: \alias{H5Dclose}

7: H5Dclose(h5dataset)

5: \title{Close an HDF5 object}

14: Close an HDF5 object

3: \name{H5Oclose}

4: \alias{H5Oclose}

7: H5Oclose(h5obj)

5: \title{Close and release a dataspace}

14: Close and release a dataspace

3: \name{H5Sclose}

4: \alias{H5Sclose}

7: H5Sclose(h5space)

11: dataspace to be closed.}

5: \title{Close access to an HDF5 file}

14: Close access to an HDF5 file

3: \name{H5Fclose}

4: \alias{H5Fclose}

7: H5Fclose(h5file)

5: \title{Close a specified group}

14: Close a specified group

3: \name{H5Gclose}

4: \alias{H5Gclose}

7: H5Gclose(h5group)

5: \title{Close an HDF5 attribute}

14: Close an HDF5 attribute

3: \name{H5Aclose}

4: \alias{H5Aclose}

7: H5Aclose(h5attribute)

11: the attribute to be closed.  Normally created by \code{\link[=H5Aopen]{H5Aopen()}} or similar.}

5: \title{Close and release a property list}

11: to close.}

3: \name{H5Pclose}

4: \alias{H5Pclose}

7: H5Pclose(h5plist)

14: \code{H5Pclose()} terminates access to a property list. All property lists

15: should be closed when they no longer need to be accessed. This

16: frees resources used by the property list.  Failing to call \code{H5Pclose()}

5: \title{Close open HDF5 handles}

20: more \linkS4class{H5IdComponent} objects and it'll will try to close all of them

27: getting to the close statement, or the open handle was not assigned to an R

42: ## close all open identifiers and verify

3: \name{h5closeAll}

4: \alias{h5closeAll}

7: h5closeAll(...)

11: closed.  If nothing is provided to the function, all open handles will be

12: closed.}

22: can be easier than making multiple calls to \code{\link[=H5Fclose]{H5Fclose()}}, \code{\link[=H5Gclose]{H5Gclose()}}, etc.

26: created and not closed correctly.  Maybe because a function stopped before

29: handles and closes them.

35: h5File <- tempfile(pattern = "ex_h5closeAll.h5")

43: h5closeAll()

3: h5File <- tempfile(pattern = "H5Close_", fileext = ".h5")

15:   ## close only the dataset

19:   ## close the file and group ids

7: test_that("Object handles can be closed", {

16:   expect_silent(h5closeAll(did))

20:   expect_silent(h5closeAll(gid, fid))

30: #' ## always close dataspaces after usage to free resources

31: #' H5Sclose(sid)

319:                                 * There is no guarantee that hint is close to actual source size */

751:     ZSTD_e_end=2       /* flush any remaining data _and_ close current frame.

1956:  * There is no guarantee that hint is close to actual source size,

752:                         * note that frame is only closed after compressed data is fully flushed (return value == 0).

1120:             /* the match was too close to the end, rewind and go to last literals */

2071:                         DEBUGLOG(7, "partialDecoding: dictionary match, close to dstEnd");

2185:                     DEBUGLOG(7, "partialDecoding: copying literals, close to input or output end")

968:    if (fp == NULL) close(fh);

360:    BZ2_bzWriteClose64 ( &bzerr, bzf, 0, 

372:       ret = fclose ( zStream );

378:    ret = fclose ( stream );

410:    BZ2_bzWriteClose64 ( &bzerr_dummy, bzf, 1, 

476:       BZ2_bzReadClose ( &bzerr, bzf );

482:    closeok:

489:    ret = fclose ( zStream );

496:       ret = fclose ( stream );

514:       goto closeok;

518:    BZ2_bzReadClose ( &bzerr_dummy, bzf );

532:          if (zStream != stdin) fclose(zStream);

533:          if (stream != stdout) fclose(stream);

591:       BZ2_bzReadClose ( &bzerr, bzf );

598:    ret = fclose ( zStream );

605:    BZ2_bzReadClose ( &bzerr_dummy, bzf );

625:          if (zStream != stdin) fclose(zStream);

708:             fclose ( outputHandleJustInCase );

944:    if (tmp != NULL) fclose ( tmp );

1019:    fclose()ing it again.  So we have to assume that the fopen() call

1250:             if ( inStr != NULL ) fclose ( inStr );

1268:             if ( inStr != NULL ) fclose ( inStr );

1275:             if ( outStr != NULL ) fclose ( outStr );

1433:             if ( inStr != NULL ) fclose ( inStr );

1445:             if ( inStr != NULL ) fclose ( inStr );

1452:             if ( outStr != NULL ) fclose ( outStr );

505:   /* Make the level 8 close enough to maxCLevel */

721:   }  /* Closes j < nsplits */

792:   } /* Closes j < nsplits */

1860:     } /* closes while (nblock_) */

735:             /* Exit fast decoding loop once we get close to the end. */

1530:             /* Exit the fast decoding loop if we are too close to the end. */

1282:     /* closer to end : up to 2 symbols at a time */

353:       // more times.  (The exception is that when we're close to exhausting

363:       // If we get close to exhausting the input then goto emit_remainder.

412:       // this loop via goto if we get close to exhausting the input.

348: Finally, you must close the bitStream.

352:     size_t size = BIT_closeCStream(&bitStream);

773:         /* close range match, overlap */

830:         /* Wildcopy until we get close to the end. */

848:         /* Handle short lengths, close overlaps, and dst not before src. */

431: /*                 /\* Close array base type *\/ */

262: /*                 H5Tclose(str_type); */

291: /*                 H5Tclose(str_type); */

292: /*                 H5Tclose(tmp_type); */

403: /*                 H5Tclose(super); */

432: /*                 H5Tclose(super); */

460:     // If match is close, let's reduce the minimum length to encode it

642:     // If match is close, let's reduce the minimum length to encode it

30: SEXP _H5close(void);

36:   {"_H5close", (DL_FUNC) &_H5close, 0},

47:   {"_H5Aclose", (DL_FUNC) &_H5Aclose, 1},

54:   {"_H5Dclose", (DL_FUNC) &_H5Dclose, 1},

65:   {"_H5Fclose", (DL_FUNC) &_H5Fclose, 1},

75:   {"_H5Gclose", (DL_FUNC) &_H5Gclose, 1},

85:   {"_H5Oclose", (DL_FUNC) &_H5Oclose, 1},

104:   {"_H5Sclose", (DL_FUNC) &_H5Sclose, 1},

138:   {"_H5Pclose", (DL_FUNC) &_H5Pclose, 1},

139:   {"_H5Pclose_class", (DL_FUNC) &_H5Pclose_class, 1},

158:   /* {"_H5Pset_fclose_degree", (DL_FUNC) &_H5Pset_fclose_degree, 2}, */

159:   /* {"_H5Pget_fclose_degree", (DL_FUNC) &_H5Pget_fclose_degree, 2}, */

794:    /*-- (emphasises close relationship of block & quadrant) --*/

11: SEXP _H5close(void);

27:     // This causes similar signed numbers close to zero to end

28:     // up close to zero in unsigned space, and compresses better

241: ...(26 bytes skipped)...SEXP _parent_class, SEXP _name, SEXP _create, SEXP _create_data, SEXP _copy, SEXP _copy_data, SEXP _close, SEXP _close_data ); */

242: ...(43 bytes skipped)...ame, SEXP _size, SEXP _default, SEXP _create, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _close ); */

243: ...(58 bytes skipped)..., SEXP _default, SEXP _create, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _compare, SEXP _close ); */

244: ...(24 bytes skipped)...P _plid, SEXP _name, SEXP _size, SEXP _value, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _close ); */

245: ...(39 bytes skipped)...name, SEXP _size, SEXP _value, SEXP _set, SEXP _get, SEXP _delete, SEXP _copy, SEXP _compare, SEXP _close ); */

19: SEXP _H5Pclose( SEXP _plist );

48: /* SEXP _H5Pset_fclose_degree( SEXP _fapl_id, SEXP _fc_degree ); */

49: /* SEXP _H5Pget_fclose_degree( SEXP _fapl_id, SEXP _fc_degree ); */

259: SEXP _H5Pclose_class( SEXP _class );

6:              close(out_file);'

6: \alias{H5close}

13: H5close()

22: \item \code{H5close} flushes all data to disk, closes all open identifiers, and cleans up memory.

33:   H5close()

34: ## rember to close open handles

19: To prevent memory leaks this must be closed with a call to \code{\link[=H5Dclose]{H5Dclose()}}

35: H5Dclose( did )

36: H5Fclose( fid )