1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
|
#############################################################################
##
## Copyright 2016 Novartis Institutes for BioMedical Research Inc.
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
##
#############################################################################
add_injection <- list(start=list(), pre_call=list(), post_call=list(), pre_list=list(), end=list())
## write injection code for H5Tset_size, that takes care of Infinity in the input
add_injection$pre_call$H5Tset_size <- c(
" // INJECTION CODE START",
" if(isReal(R_size ) && REAL(R_size)[0] == R_PosInf) {",
" size = H5T_VARIABLE;",
" }",
" // INJECTION CODE END"
)
add_injection$pre_call$H5Sset_extent_simple <- c(
" // INJECTION CODE START",
" // the pointer is to const; need to cast it when I detect an Inf value",
" if(isReal(R_max)) {",
" hsize_t* max_helper = (hsize_t *) VOIDPTR(R_helper);",
" for(int i=0; i < rank; ++i) {",
" if(REAL(R_max)[i] == R_PosInf) {",
" max_helper[i] = H5S_UNLIMITED;",
" }",
" }",
" }",
" // INJECTION CODE END"
)
add_injection$pre_call$H5Screate_simple <- c(
" // INJECTION CODE START",
" // the pointer is to const; need to cast it when I detect an Inf value",
" if(isReal(R_maxdims)) {",
" hsize_t* maxdims_helper = (hsize_t *) VOIDPTR(R_helper);",
" for(int i=0; i < rank; ++i) {",
" if(REAL(R_maxdims)[i] == R_PosInf) {",
" maxdims_helper[i] = H5S_UNLIMITED;",
" }",
" }",
" }",
" // INJECTION CODE END"
)
add_injection$pre_list$H5Sget_simple_extent_dims <- c(
" // INJECTION CODE START",
" // check if it is an int64 vector, and if yes which is H5S_UNLIMITED",
" // in that case, the return needs to be a real vector, so that Inf can be set",
" if(is_rint64(R_maxdims)) {",
" R_maxdims = PROTECT(convert_int64_using_flags(R_maxdims, H5TOR_CONV_INT64_FLOAT_FORCE));",
" vars_protected++;",
" double dbl_unlimited = (double) LLONG_MAX;",
" R_xlen_t len = XLENGTH(R_maxdims);",
" for(R_xlen_t i = 0; i < len; ++i) {",
" if(REAL(R_maxdims)[i] == dbl_unlimited) {",
" REAL(R_maxdims)[i] = R_PosInf;",
" }",
" }",
" }",
" // INJECTION CODE END"
)
add_injection$pre_call$H5Pset_chunk_cache <- c(
" // INJECTION CODE START",
" if(SEXP_to_longlong(R_rdcc_nslots, 0)==-1) {",
" rdcc_nslots = H5D_CHUNK_CACHE_NSLOTS_DEFAULT;",
" }",
" if(SEXP_to_longlong(R_rdcc_nbytes, 0)==-1) {",
" rdcc_nbytes = H5D_CHUNK_CACHE_NBYTES_DEFAULT;",
" }",
" if(SEXP_to_longlong(R_rdcc_w0, 0)==-1) {",
" rdcc_w0 = H5D_CHUNK_CACHE_W0_DEFAULT;",
" }",
" // INJECTION CODE END"
)
|
