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Changes to documentation to fix broken links
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The HDF5 website recently moved so that all links were broken.

Here we replace the links. As the links to the particular functions itself are hash-codes now,
only links to the pages of the function-groups are provided.
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@hhoeflin
hhoeflin committed Mar 2, 2024
1 parent d1923a9 commit cdf3484
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Showing 141 changed files with 10,311 additions and 13,959 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: hdf5r
Type: Package
Title: Interface to the 'HDF5' Binary Data Format
Version: 1.3.9
Version: 1.3.10
Authors@R: c(
person("Holger", "Hoefling", email = "[email protected]", role = c("aut", "cre")),
person("Mario", "Annau", email = "[email protected]", role = "aut"),
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122 changes: 61 additions & 61 deletions R/Common_functions.R
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2 changes: 1 addition & 1 deletion R/R6Classes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ H5RefClass <- R6Class("H5RefClass",
},
is_valid=function() {
"This function implements the HDF5-API function H5Iis_valid."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5I_IS_VALID} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_i.html} for details."
"Additionally, the R-object representing the HDF5-id can be invalidated as well. In this"
"case, the class id is set to \\code{NA} and \\code{is_valid} returns \\code{FALSE}."

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14 changes: 7 additions & 7 deletions R/R6Classes_H5A.R
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ H5A <- R6Class("H5A",
public=list(
get_info=function() {
"This function implements the HDF5-API function H5Aget_info."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_GET_INFO} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

res <- .Call("R_H5Aget_info", self$id, request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
Expand All @@ -63,7 +63,7 @@ H5A <- R6Class("H5A",
},
attr_name=function() {
"This function implements the HDF5-API function H5Aget_name."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_GET_NAME} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

## get size of the name
name_size <- .Call("R_H5Aget_name", self$id, 0, character(0), PACKAGE="hdf5r")$return_val
Expand All @@ -83,7 +83,7 @@ H5A <- R6Class("H5A",
},
get_space=function() {
"This function implements the HDF5-API function H5Aget_space."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_GET_SPACE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

id <- .Call("R_H5Aget_space", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
Expand All @@ -93,7 +93,7 @@ H5A <- R6Class("H5A",
},
get_type=function(native=TRUE) {
"This function implements the HDF5-API function H5Aget_type."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_GET_TYPE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

id <- .Call("R_H5Aget_type", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
Expand All @@ -114,15 +114,15 @@ H5A <- R6Class("H5A",
},
get_storage_size=function() {
"This function implements the HDF5-API function H5Aget_storage_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_GET_STORAGE_SIZE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

size <- .Call("R_H5Aget_storage_size", self$id, PACKAGE="hdf5r")$return_val
return(size)
},
read_low_level=function(buffer, mem_type, duplicate_buffer=FALSE) {
"Only for advanced users. See documentation for \\code{read} instead."
"This function implements the HDF5-API function H5Aread."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_READ} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

check_class(mem_type, "H5T")
res <- .Call("R_H5Aread", self$id, mem_type$id, buffer, duplicate_buffer, PACKAGE="hdf5r")
Expand Down Expand Up @@ -183,7 +183,7 @@ H5A <- R6Class("H5A",
write_low_level=function(buffer, mem_type) {
"Only for advanced users. See documentation for \\code{write} instead."
"This function implements the HDF5-API function H5Awrite."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5A_WRITE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_a.html} for details."

check_class(mem_type, "H5T")
res <- .Call("R_H5Awrite", self$id, mem_type$id, buffer, PACKAGE="hdf5r")
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28 changes: 14 additions & 14 deletions R/R6Classes_H5D.R
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ H5D <- R6Class("H5D",
},
get_space=function() {
"This function implements the HDF5-API function H5Dget_space."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_SPACE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

id <- .Call("R_H5Dget_space", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
Expand All @@ -120,7 +120,7 @@ H5D <- R6Class("H5D",
},
get_space_status=function() {
"This function implements the HDF5-API function H5Dget_space_status."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_SPACE_STATUS} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

res <- .Call("R_H5Dget_space_status", self$id, request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
Expand All @@ -130,14 +130,14 @@ H5D <- R6Class("H5D",
},
get_type=function(native=TRUE) {
"This function implements the HDF5-API function H5Dget_type."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_TYPE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

id <- standalone_H5D_get_type(h5d_id=self$id, native=native)
return(H5T_factory(id))
},
get_create_plist=function() {
"This function implements the HDF5-API function H5Dget_create_plist."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_CREATE_PLIST} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

id <- .Call("R_H5Dget_create_plist", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
Expand All @@ -147,7 +147,7 @@ H5D <- R6Class("H5D",
},
get_access_plist=function() {
"This function implements the HDF5-API function H5Dget_access_plist."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_ACCESS_PLIST} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

id <- .Call("R_H5Dget_access_plist", self$id, PACKAGE="hdf5r")$return_val
if(id < 0) {
Expand All @@ -157,7 +157,7 @@ H5D <- R6Class("H5D",
},
get_offset=function() {
"This function implements the HDF5-API function H5Dget_offset."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_OFFSET} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

haddr <- .Call("R_H5Dget_offset", self$id, PACKAGE="hdf5r")$return_val
if(haddr < 0) {
Expand All @@ -167,14 +167,14 @@ H5D <- R6Class("H5D",
},
get_storage_size=function() {
"This function implements the HDF5-API function H5Dget_storage_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_GET_STORAGE_SIZE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

size <- .Call("R_H5Dget_storage_size", self$id, PACKAGE="hdf5r")$return_val
return(size)
},
vlen_get_buf_size=function(type, space) {
"This function implements the HDF5-API function H5Dvlen_get_buf_size."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_VLEN_GET_BUF_SIZE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

check_class(type, "H5T")
check_class(space, "H5S")
Expand All @@ -187,7 +187,7 @@ H5D <- R6Class("H5D",
},
vlen_reclaim=function(buffer, type, space, dataset_xfer_pl=h5const$H5P_DEFAULT) {
"This function implements the HDF5-API function H5Dvlen_reclaim."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_VLEN_RECLAIM} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

check_class(type, "H5T")
check_class(space, "H5S")
Expand All @@ -203,7 +203,7 @@ H5D <- R6Class("H5D",
dataset_xfer_pl=h5const$H5P_DEFAULT, flags=getOption("hdf5r.h5tor_default"), set_dim=FALSE, dim_to_set=NULL, drop=TRUE) {
"This function is for advanced users. It is recommended to use \\code{read} instead or the \\code{[} interface."
"This function implements the HDF5-API function H5Dread, with minor changes to the API to accommodate R."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_READ} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."
"It reads the data in the dataset as specified by \\code{mem_space} and return it as an R-obj"
"@param file_space An HDF5-space, represented as class \\code{\\link{H5S}} that determines which part"
"of the dataset is being read. Can also be given as an id"
Expand Down Expand Up @@ -397,7 +397,7 @@ H5D <- R6Class("H5D",
"This function is for advanced users. It is recommended to use \\code{read} instead or the \\code{[<-} interface"
"as used for arrays."
"This function implements the HDF5-API function H5Dwrite, with some changes to accommodate R."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_WRITE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."
"It writes that data from the \\code{robj} into the dataset."
"@param robj The object to write into the dataset"
"@param mem_space The space as it is represented in memory; advanced feature; may be removed in the future"
Expand Down Expand Up @@ -573,7 +573,7 @@ H5D <- R6Class("H5D",
},
set_extent=function(dims) {
"This function implements the HDF5-API function H5Dset_extent."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5D_SET_EXTENT} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_d.html} for details."

rank <- self$get_space()$get_simple_extent_ndims()
if(length(dims) != rank) {
Expand All @@ -588,7 +588,7 @@ H5D <- R6Class("H5D",
get_fill_value=function() {
"This function implements the HDF5-API function H5Pget_fill_value, automatically"
"supplying the datatype of the dataset for convenience."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5P_GET_FILL_VALUE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_p.html} for details."

dtype <- self$get_type()
create_plist <- self$get_create_plist()
Expand All @@ -602,7 +602,7 @@ H5D <- R6Class("H5D",
create_reference=function(...) {
"This function implements the HDF5-API function H5Rcreate. The parameters are interpreted as in '['."
"The function always create \\code{H5R_DATASET_REGION} references"
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5R_CREATE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_r.html} for details."

space <- self$get_space()
do.call("[", c(list(space), list(...)))
Expand Down
10 changes: 5 additions & 5 deletions R/R6Classes_H5File.R
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Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,7 @@ H5File <- R6Class("H5File",
},
get_obj_count=function(types=h5const$H5F_OBJ_ALL) {
"This function implements the HDF5-API function H5Fget_obj_count."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5F_GET_OBJ_COUNT} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_f.html} for details."
count <- .Call("R_H5Fget_obj_count", self$id, types, PACKAGE = "hdf5r")$return_val
if(count < 0) {
stop("Couldn't get object count in file")
Expand All @@ -200,7 +200,7 @@ H5File <- R6Class("H5File",
},
get_obj_ids=function(types=h5const$H5F_OBJ_ALL) {
"This function implements the HDF5-API function H5Fget_obj_ids."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5F_GET_OBJ_IDS} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_f.html} for details."

count <- self$get_obj_count(types=types)
res <- .Call("R_H5Fget_obj_ids", self$id, types, count, request_empty(count), PACKAGE = "hdf5r")
Expand All @@ -212,7 +212,7 @@ H5File <- R6Class("H5File",
},
get_filesize=function() {
"This function implements the HDF5-API function H5Fget_filesize."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5F_GET_FILESIZE} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_f.html} for details."

res <- .Call("R_H5Fget_filesize", self$id, request_empty(1), PACKAGE = "hdf5r")
if(res$return_val < 0) {
Expand All @@ -222,7 +222,7 @@ H5File <- R6Class("H5File",
},
file_info=function() {
"This function implements the HDF5-API function H5Fget_info2."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5F_GET_INFO2} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_f.html} for details."
"Please note that the returned information differs if HDF5 Version 1.8.16 or HDF5 Version >= 1.10.0 is being used"

if(is.loaded("R_H5Fget_info2", PACKAGE = "hdf5r")) {
Expand All @@ -242,7 +242,7 @@ H5File <- R6Class("H5File",
},
get_intent=function() {
"This function implements the HDF5-API function H5Fget_intent."
"Please see the documentation at \\url{https://portal.hdfgroup.org/display/HDF5/H5F_GET_INTENT} for details."
"Please see the documentation at \\url{https://docs.hdfgroup.org/hdf5/develop/group___h5_f.html} for details."

res <- .Call("R_H5Fget_intent", self$id, request_empty(1), PACKAGE="hdf5r")
if(res$return_val < 0) {
Expand Down
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