1. rhdf5client
  2. NAMESPACE
Browse code

basic compound support

Alexey Sergushichev authored on 21/03/2023 02:30:59
Showing 1 changed files
NAMESPACE
History View file @ 6722a72
... ... 
@@ -18,5 +18,7 @@ import(httr)
18 18 
 import(methods)
19 19 
 import(rjson)
20 20 
 importFrom(DelayedArray,new_DelayedArray)
21 
+importFrom(data.table,as.data.table)
22 
+importFrom(data.table,rbindlist)
21 23 
 importFrom(utils,strcapture)
22 24 
 useDynLib(rhdf5client, .registration = TRUE)
Browse code

pushing default transfermode binary

vjcitn authored on 06/01/2023 21:51:57
Showing 1 changed files
NAMESPACE
History View file @ 383de61
... ... 
@@ -1,64 +1,22 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export("transfermode<-")
4 
-export(H5S_Array)
5 
-export(H5S_dataset2)
6 
-export(H5S_source)
7 3 
 export(HSDSArray)
8 4 
 export(HSDSDataset)
9 5 
 export(HSDSFile)
10 6 
 export(HSDSSource)
11 
-export(HSDS_Matrix)
12 
-export(HSDS_Matrix_OLD)
13 
-export(URL_h5serv)
14 7 
 export(URL_hsds)
15 8 
 export(check_hsds)
16 
-export(dataset)
17 
-export(domains)
18 
-export(dsmeta)
19 
-export(fetchDatasets)
20 9 
 export(getData)
21 
-export(getDatasetAttrs)
22 
-export(getDatasetSlice)
23 
-export(getDatasetUUIDs)
24 
-export(getDims)
25 
-export(getHRDF)
26 
-export(getReq)
27 
-export(groups)
28 
-export(hsdsInfo)
29 
-export(internalDim)
30 10 
 export(isplit)
31 
-export(links)
32 11 
 export(listDatasets)
33 12 
 export(listDomains)
34 
-export(setPath)
35 13 
 export(sproc)
36 
-export(targets)
37 
-exportClasses(H5S_Array)
38 
-exportClasses(H5S_Matrix)
39 
-exportClasses(H5S_dataset)
40 
-exportClasses(H5S_source)
41 14 
 exportClasses(HSDSArray)
42 15 
 exportClasses(HSDSMatrix)
43 
-exportMethods("[")
44 
-exportMethods('[[')
45 
-exportMethods(dim)
46 
-exportMethods(dimnames)
47 
-exportMethods(domains)
48 
-exportMethods(groups)
49 
-exportMethods(hsdsInfo)
50 
-exportMethods(links)
51 
-exportMethods(setPath)
52 16 
 import(DelayedArray)
53 
-import(R6)
54 
-import(S4Vectors)
55 17 
 import(httr)
56 18 
 import(methods)
57 19 
 import(rjson)
58 20 
 importFrom(DelayedArray,new_DelayedArray)
59 
-importFrom(httr,GET)
60 
-importFrom(httr,add_headers)
61 
-importFrom(rjson,fromJSON)
62 
-importFrom(utils,capture.output)
63 21 
 importFrom(utils,strcapture)
64 22 
 useDynLib(rhdf5client, .registration = TRUE)
Browse code

introduce condition to check for HSDS service

vjcitn authored on 17/05/2021 20:08:47
Showing 1 changed files
NAMESPACE
History View file @ 57f815b
... ... 
@@ -12,6 +12,7 @@ export(HSDS_Matrix)
12 12 
 export(HSDS_Matrix_OLD)
13 13 
 export(URL_h5serv)
14 14 
 export(URL_hsds)
15 
+export(check_hsds)
15 16 
 export(dataset)
16 17 
 export(domains)
17 18 
 export(dsmeta)
Browse code

Documentation fix to remove WARNING about double-subscript function

Samuela Pollack authored on 12/04/2019 15:37:48
Showing 1 changed files
NAMESPACE
History View file @ bd4ca47
... ... 
@@ -40,7 +40,7 @@ exportClasses(H5S_source)
40 40 
 exportClasses(HSDSArray)
41 41 
 exportClasses(HSDSMatrix)
42 42 
 exportMethods("[")
43 
-exportMethods("[[")
43 
+exportMethods('[[')
44 44 
 exportMethods(dim)
45 45 
 exportMethods(dimnames)
46 46 
 exportMethods(domains)
Browse code

Documentation changes to eliminate warnings

Samuela Pollack authored on 23/10/2018 18:35:02
Showing 1 changed files
NAMESPACE
History View file @ fca711a
... ... 
@@ -12,7 +12,6 @@ export(HSDS_Matrix)
12 12 
 export(HSDS_Matrix_OLD)
13 13 
 export(URL_h5serv)
14 14 
 export(URL_hsds)
15 
-export(as)
16 15 
 export(dataset)
17 16 
 export(domains)
18 17 
 export(dsmeta)
Browse code

Added rhdf5client2 tests; miscellaneous small fixes to remove warnings

Samuela Pollack authored on 23/10/2018 17:50:04
Showing 1 changed files
NAMESPACE
History View file @ a04ab93
... ... 
@@ -5,7 +5,6 @@ export(H5S_Array)
5 5 
 export(H5S_dataset2)
6 6 
 export(H5S_source)
7 7 
 export(HSDSArray)
8 
-export(HSDSArraySeed)
9 8 
 export(HSDSDataset)
10 9 
 export(HSDSFile)
11 10 
 export(HSDSSource)
... ... 
@@ -40,14 +39,12 @@ exportClasses(H5S_Matrix)
40 39 
 exportClasses(H5S_dataset)
41 40 
 exportClasses(H5S_source)
42 41 
 exportClasses(HSDSArray)
43 
-exportClasses(HSDSArraySeed)
44 42 
 exportClasses(HSDSMatrix)
45 43 
 exportMethods("[")
46 44 
 exportMethods("[[")
47 45 
 exportMethods(dim)
48 46 
 exportMethods(dimnames)
49 47 
 exportMethods(domains)
50 
-exportMethods(extract_array)
51 48 
 exportMethods(groups)
52 49 
 exportMethods(hsdsInfo)
53 50 
 exportMethods(links)
... ... 
@@ -64,4 +61,4 @@ importFrom(httr,add_headers)
64 61 
 importFrom(rjson,fromJSON)
65 62 
 importFrom(utils,capture.output)
66 63 
 importFrom(utils,strcapture)
67 
-useDynLib(rhdf5client)
64 
+useDynLib(rhdf5client, .registration = TRUE)
Browse code

resolved conflicting name 'domains'

Samuela Pollack authored on 22/10/2018 20:34:00
Showing 1 changed files
NAMESPACE
History View file @ 45a9390
... ... 
@@ -31,6 +31,7 @@ export(internalDim)
31 31 
 export(isplit)
32 32 
 export(links)
33 33 
 export(listDatasets)
34 
+export(listDomains)
34 35 
 export(setPath)
35 36 
 export(sproc)
36 37 
 export(targets)
... ... 
@@ -51,7 +52,6 @@ exportMethods(groups)
51 52 
 exportMethods(hsdsInfo)
52 53 
 exportMethods(links)
53 54 
 exportMethods(setPath)
54 
-import(BiocGenerics)
55 55 
 import(DelayedArray)
56 56 
 import(R6)
57 57 
 import(S4Vectors)
Browse code

Modifications necessary to make vignettes build

User-Zero authored on 02/10/2018 16:30:08
Showing 1 changed files
NAMESPACE
History View file @ f759141
... ... 
@@ -64,4 +64,4 @@ importFrom(httr,add_headers)
64 64 
 importFrom(rjson,fromJSON)
65 65 
 importFrom(utils,capture.output)
66 66 
 importFrom(utils,strcapture)
67 
-useDynLib(rhdf5client2)
67 
+useDynLib(rhdf5client)
Browse code

Added rhdf5client2 code to package

User-Zero authored on 02/10/2018 15:15:10
Showing 1 changed files
NAMESPACE
History View file @ 2c9b8e9
... ... 
@@ -4,7 +4,13 @@ export("transfermode<-")
4 4 
 export(H5S_Array)
5 5 
 export(H5S_dataset2)
6 6 
 export(H5S_source)
7 
+export(HSDSArray)
8 
+export(HSDSArraySeed)
9 
+export(HSDSDataset)
10 
+export(HSDSFile)
11 
+export(HSDSSource)
7 12 
 export(HSDS_Matrix)
13 
+export(HSDS_Matrix_OLD)
8 14 
 export(URL_h5serv)
9 15 
 export(URL_hsds)
10 16 
 export(as)
... ... 
@@ -12,6 +18,7 @@ export(dataset)
12 18 
 export(domains)
13 19 
 export(dsmeta)
14 20 
 export(fetchDatasets)
21 
+export(getData)
15 22 
 export(getDatasetAttrs)
16 23 
 export(getDatasetSlice)
17 24 
 export(getDatasetUUIDs)
... ... 
@@ -23,6 +30,7 @@ export(hsdsInfo)
23 30 
 export(internalDim)
24 31 
 export(isplit)
25 32 
 export(links)
33 
+export(listDatasets)
26 34 
 export(setPath)
27 35 
 export(sproc)
28 36 
 export(targets)
... ... 
@@ -30,22 +38,30 @@ exportClasses(H5S_Array)
30 38 
 exportClasses(H5S_Matrix)
31 39 
 exportClasses(H5S_dataset)
32 40 
 exportClasses(H5S_source)
41 
+exportClasses(HSDSArray)
42 
+exportClasses(HSDSArraySeed)
43 
+exportClasses(HSDSMatrix)
33 44 
 exportMethods("[")
34 45 
 exportMethods("[[")
35 46 
 exportMethods(dim)
36 47 
 exportMethods(dimnames)
37 48 
 exportMethods(domains)
49 
+exportMethods(extract_array)
38 50 
 exportMethods(groups)
39 51 
 exportMethods(hsdsInfo)
40 52 
 exportMethods(links)
41 53 
 exportMethods(setPath)
54 
+import(BiocGenerics)
42 55 
 import(DelayedArray)
43 56 
 import(R6)
44 57 
 import(S4Vectors)
45 58 
 import(httr)
46 59 
 import(methods)
60 
+import(rjson)
47 61 
 importFrom(DelayedArray,new_DelayedArray)
48 62 
 importFrom(httr,GET)
49 63 
 importFrom(httr,add_headers)
50 64 
 importFrom(rjson,fromJSON)
51 65 
 importFrom(utils,capture.output)
66 
+importFrom(utils,strcapture)
67 
+useDynLib(rhdf5client2)
Browse code

Modified roxygen to remove Bioconductor warnings

Samuela Pollack authored on 19/08/2018 21:24:22
Showing 1 changed files
NAMESPACE
History View file @ 999c3a2
... ... 
@@ -1,13 +1,13 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export("transfermode<-")
4 
-export()
5 4 
 export(H5S_Array)
6 5 
 export(H5S_dataset2)
7 6 
 export(H5S_source)
8 7 
 export(HSDS_Matrix)
9 8 
 export(URL_h5serv)
10 9 
 export(URL_hsds)
10 
+export(as)
11 11 
 export(dataset)
12 12 
 export(domains)
13 13 
 export(dsmeta)
Browse code

minor changes

shwetagopaul authored on 09/08/2018 15:56:32
Showing 1 changed files
NAMESPACE
History View file @ a64fd1a
... ... 
@@ -40,7 +40,9 @@ exportMethods(hsdsInfo)
40 40 
 exportMethods(links)
41 41 
 exportMethods(setPath)
42 42 
 import(DelayedArray)
43 
+import(R6)
43 44 
 import(S4Vectors)
45 
+import(httr)
44 46 
 import(methods)
45 47 
 importFrom(DelayedArray,new_DelayedArray)
46 48 
 importFrom(httr,GET)
Browse code

Functionality to work with multiple datasets in a hdf5 file, version bump 1.3.7

shwetagopaul authored on 08/08/2018 15:43:05
Showing 1 changed files
NAMESPACE
History View file @ 450bfd7
... ... 
@@ -11,6 +11,7 @@ export(URL_hsds)
11 11 
 export(dataset)
12 12 
 export(domains)
13 13 
 export(dsmeta)
14 
+export(fetchDatasets)
14 15 
 export(getDatasetAttrs)
15 16 
 export(getDatasetSlice)
16 17 
 export(getDatasetUUIDs)
Browse code

making code compatibile with new hsds (hdflab) version bump 1.1.4

shwetagopaul authored on 23/07/2018 17:03:04
Showing 1 changed files
NAMESPACE
History View file @ c9aff58
... ... 
@@ -41,6 +41,7 @@ exportMethods(setPath)
41 41 
 import(DelayedArray)
42 42 
 import(S4Vectors)
43 43 
 import(methods)
44 
+importFrom(DelayedArray,new_DelayedArray)
44 45 
 importFrom(httr,GET)
45 46 
 importFrom(httr,add_headers)
46 47 
 importFrom(rjson,fromJSON)
Browse code

adding HSDS_Matrix.R

Vince Carey authored on 16/05/2018 01:27:48
Showing 1 changed files
NAMESPACE
History View file @ 4aa5bbc
... ... 
@@ -5,6 +5,7 @@ export()
5 5 
 export(H5S_Array)
6 6 
 export(H5S_dataset2)
7 7 
 export(H5S_source)
8 
+export(HSDS_Matrix)
8 9 
 export(URL_h5serv)
9 10 
 export(URL_hsds)
10 11 
 export(dataset)
Browse code

fix some problems, use URL_h5serv() and URL_hsds() to limit use of URL constants throughout examples, tests, and vignettes

Vince Carey authored on 02/05/2018 02:23:20
Showing 1 changed files
NAMESPACE
History View file @ f19f0e5
... ... 
@@ -5,6 +5,8 @@ export()
5 5 
 export(H5S_Array)
6 6 
 export(H5S_dataset2)
7 7 
 export(H5S_source)
8 
+export(URL_h5serv)
9 
+export(URL_hsds)
8 10 
 export(dataset)
9 11 
 export(domains)
10 12 
 export(dsmeta)
Browse code

moving H5S_Array to this package, and introducing new vignette

Vince Carey authored on 19/03/2018 18:57:47
Showing 1 changed files
NAMESPACE
History View file @ 95bb63c
... ... 
@@ -1,6 +1,8 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export("transfermode<-")
4 
+export()
5 
+export(H5S_Array)
4 6 
 export(H5S_dataset2)
5 7 
 export(H5S_source)
6 8 
 export(dataset)
... ... 
@@ -20,15 +22,20 @@ export(links)
20 22 
 export(setPath)
21 23 
 export(sproc)
22 24 
 export(targets)
25 
+exportClasses(H5S_Array)
26 
+exportClasses(H5S_Matrix)
23 27 
 exportClasses(H5S_dataset)
24 28 
 exportClasses(H5S_source)
25 29 
 exportMethods("[")
26 30 
 exportMethods("[[")
31 
+exportMethods(dim)
32 
+exportMethods(dimnames)
27 33 
 exportMethods(domains)
28 34 
 exportMethods(groups)
29 35 
 exportMethods(hsdsInfo)
30 36 
 exportMethods(links)
31 37 
 exportMethods(setPath)
38 
+import(DelayedArray)
32 39 
 import(S4Vectors)
33 40 
 import(methods)
34 41 
 importFrom(httr,GET)
Browse code

adding setPath method

shwetagopaul authored on 31/01/2018 20:48:10
Showing 1 changed files
NAMESPACE
History View file @ fe80070
... ... 
@@ -17,6 +17,7 @@ export(hsdsInfo)
17 17 
 export(internalDim)
18 18 
 export(isplit)
19 19 
 export(links)
20 
+export(setPath)
20 21 
 export(sproc)
21 22 
 export(targets)
22 23 
 exportClasses(H5S_dataset)
... ... 
@@ -27,6 +28,7 @@ exportMethods(domains)
27 28 
 exportMethods(groups)
28 29 
 exportMethods(hsdsInfo)
29 30 
 exportMethods(links)
31 
+exportMethods(setPath)
30 32 
 import(S4Vectors)
31 33 
 import(methods)
32 34 
 importFrom(httr,GET)
Browse code

some changes to hsds code

shwetagopaul authored on 31/01/2018 19:04:08
Showing 1 changed files
NAMESPACE
History View file @ 317c907
... ... 
@@ -13,15 +13,10 @@ export(getDims)
13 13 
 export(getHRDF)
14 14 
 export(getReq)
15 15 
 export(groups)
16 
-export(hsdel)
17 
-export(hsget)
18 
-export(hsload)
19 
-export(hsls)
20 
-export(hstouch)
16 
+export(hsdsInfo)
21 17 
 export(internalDim)
22 18 
 export(isplit)
23 19 
 export(links)
24 
-export(setCredentials)
25 20 
 export(sproc)
26 21 
 export(targets)
27 22 
 exportClasses(H5S_dataset)
... ... 
@@ -29,8 +24,8 @@ exportClasses(H5S_source)
29 24 
 exportMethods("[")
30 25 
 exportMethods("[[")
31 26 
 exportMethods(domains)
32 
-exportMethods(getReq)
33 27 
 exportMethods(groups)
28 
+exportMethods(hsdsInfo)
34 29 
 exportMethods(links)
35 30 
 import(S4Vectors)
36 31 
 import(methods)
Browse code

adding hsds code, version bump to 1.1.7

shwetagopaul authored on 25/01/2018 16:23:33
Showing 1 changed files
NAMESPACE
History View file @ 52eb601
... ... 
@@ -1,19 +1,35 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export("transfermode<-")
4 
+export(H5S_dataset2)
4 5 
 export(H5S_source)
5 6 
 export(dataset)
7 
+export(domains)
6 8 
 export(dsmeta)
9 
+export(getDatasetAttrs)
10 
+export(getDatasetSlice)
11 
+export(getDatasetUUIDs)
12 
+export(getDims)
13 
+export(getHRDF)
14 
+export(getReq)
7 15 
 export(groups)
16 
+export(hsdel)
17 
+export(hsget)
18 
+export(hsload)
19 
+export(hsls)
20 
+export(hstouch)
8 21 
 export(internalDim)
9 22 
 export(isplit)
10 23 
 export(links)
24 
+export(setCredentials)
11 25 
 export(sproc)
12 26 
 export(targets)
13 27 
 exportClasses(H5S_dataset)
14 28 
 exportClasses(H5S_source)
15 29 
 exportMethods("[")
16 30 
 exportMethods("[[")
31 
+exportMethods(domains)
32 
+exportMethods(getReq)
17 33 
 exportMethods(groups)
18 34 
 exportMethods(links)
19 35 
 import(S4Vectors)
Browse code

documentation change, no need to export ivindx

Samuela Pollack authored on 26/10/2017 13:55:37
Showing 1 changed files
NAMESPACE
History View file @ 940325d
... ... 
@@ -7,7 +7,6 @@ export(dsmeta)
7 7 
 export(groups)
8 8 
 export(internalDim)
9 9 
 export(isplit)
10 
-export(ivindx)
11 10 
 export(links)
12 11 
 export(sproc)
13 12 
 export(targets)
Browse code

implementation of negative indices

Samuela Pollack authored on 17/10/2017 16:52:12
Showing 1 changed files
NAMESPACE
History View file @ 6a7036a
... ... 
@@ -7,6 +7,7 @@ export(dsmeta)
7 7 
 export(groups)
8 8 
 export(internalDim)
9 9 
 export(isplit)
10 
+export(ivindx)
10 11 
 export(links)
11 12 
 export(sproc)
12 13 
 export(targets)
Browse code

Miscellaneous R improvements suggested by Bioconductor review

Samuela Pollack authored on 12/09/2017 20:53:14
Showing 1 changed files
NAMESPACE
History View file @ 360fd51
... ... 
@@ -21,3 +21,4 @@ import(methods)
21 21 
 importFrom(httr,GET)
22 22 
 importFrom(httr,add_headers)
23 23 
 importFrom(rjson,fromJSON)
24 
+importFrom(utils,capture.output)
Browse code

Changes to documentation and vignettes necessary to pass BiocCheck and devtools::check

Samuela Pollack authored on 10/08/2017 18:06:31
Showing 1 changed files
NAMESPACE
History View file @ d135590
... ... 
@@ -9,7 +9,6 @@ export(internalDim)
9 9 
 export(isplit)
10 10 
 export(links)
11 11 
 export(sproc)
12 
-export(submatrix)
13 12 
 export(targets)
14 13 
 exportClasses(H5S_dataset)
15 14 
 exportClasses(H5S_source)
Browse code

Added transfer mode property to H5S_dataset to facilitate profiling and profiling script. Also fixed bug in indexing method for returning JSON output in a matrix.

Samuela Pollack authored on 14/07/2017 15:08:12
Showing 1 changed files
NAMESPACE
History View file @ e1f1f8d
... ... 
@@ -1,5 +1,6 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export("transfermode<-")
3 4 
 export(H5S_source)
4 5 
 export(dataset)
5 6 
 export(dsmeta)
Browse code

Initial commit

Samuela Pollack authored on 06/07/2017 19:45:29
Showing 1 changed files
NAMESPACE
History View file @ b769b2a
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,23 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(H5S_source)
4 
+export(dataset)
5 
+export(dsmeta)
6 
+export(groups)
7 
+export(internalDim)
8 
+export(isplit)
9 
+export(links)
10 
+export(sproc)
11 
+export(submatrix)
12 
+export(targets)
13 
+exportClasses(H5S_dataset)
14 
+exportClasses(H5S_source)
15 
+exportMethods("[")
16 
+exportMethods("[[")
17 
+exportMethods(groups)
18 
+exportMethods(links)
19 
+import(S4Vectors)
20 
+import(methods)
21 
+importFrom(httr,GET)
22 
+importFrom(httr,add_headers)
23 
+importFrom(rjson,fromJSON)