version 0.0.3

cran · Nov 6, 2023 · c9f75fa · c9f75fa
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: hdf5r.Extra
 Type: Package
 Title: Extensions for 'HDF5' R Interfaces
-Version: 0.0.2
-Date: 2023-09-21
+Version: 0.0.3
+Date: 2023-10-19
 Authors@R: person(given = "Yuchen", family = "Li", email = "ycli1995@outlook.com", role = c("aut", "cre"))
 Description: Some methods to manipulate 'HDF5' files, extending the 'hdf5r' package. Reading and writing R objects to 'HDF5' formats follow the specification of 'AnnData' <https://anndata.readthedocs.io/en/latest/fileformat-prose.html>.
 Depends: R (>= 4.1.0), hdf5r (>= 1.3.8), methods, utils
@@ -13,8 +13,8 @@ Encoding: UTF-8
 URL: https://github.com/ycli1995/hdf5r.Extra
 BugReports: https://github.com/ycli1995/hdf5r.Extra/issues
 NeedsCompilation: no
-Packaged: 2023-09-22 05:07:50 UTC; mydocker
+Packaged: 2023-11-06 09:22:01 UTC; mydocker
 Author: Yuchen Li [aut, cre]
 Maintainer: Yuchen Li <ycli1995@outlook.com>
 Repository: CRAN
-Date/Publication: 2023-09-22 07:30:02 UTC
+Date/Publication: 2023-11-06 09:40:02 UTC
diff --git a/MD5 b/MD5
@@ -1,16 +1,16 @@
-092ba5a9d231d26ff9318433cb2a6a22 *DESCRIPTION
+04a31218bca95f9e969271734505e1c3 *DESCRIPTION
 1285b0f228eef791319304295b0184fc *LICENSE
-46afd66ee3b76c30a741a802b42432f8 *NAMESPACE
-8a70b484241314a464dc9a908c33d14f *NEWS.md
+7a1b18844d91d0cb08d4cd1f6e3b69b4 *NAMESPACE
+ee4f0fd399ca4698fe3e0e88795ff60a *NEWS.md
 5350e6ab1434ccd0a70dfa1562af2f8b *R/AllGenerics.R
-8bbd664ea2fa7923921b15716f4a0f26 *R/hdf5-functions.R
-f2b9c56104d1562ca1a4675b6e7fb968 *R/hdf5-internal.R
-0a7c3b98617a7270176c9337603aa092 *R/hdf5-methods.R
+4fd2186b9ebae5f440e8c0299788cc27 *R/hdf5-functions.R
+743f008608c7e7f7959c63dac97460e1 *R/hdf5-internal.R
+872bf803358ce542a8bca26d661777c4 *R/hdf5-methods.R
 c79087585c3cb97e93603e4637db4e6d *R/zzz.R
 d3f437597544eedce65892287c06d94b *README.md
 e28ff15653d6ad6c23682246a76fcd04 *inst/extdata/pbmc_small.h5ad
 3148c7d9176dc65616bee55654c3451e *man/H5-attributs.Rd
-3463e52b5f70b410cb148b854de4c130 *man/H5-dataset-info.Rd
+993517368aa1f3d01bde03c4c28d8188 *man/H5-dataset-info.Rd
 be8266f09349e8e3a2a843a179b4e213 *man/h5AbsLinkName.Rd
 4e8da2fb480dcb9b99bc18111d78eb8f *man/h5Backup.Rd
 4002d9bfe316fb247f5249b556b6fc22 *man/h5Class.Rd
@@ -26,7 +26,7 @@ b633edf99a57afe4ba05d9d70151e28f *man/h5CreateGroup.Rd
 3faf6f1047eb373131a5c5d6b85c71c6 *man/h5Open.Rd
 d43a4069a214e44352f0d002d2285e50 *man/h5Overwrite.Rd
 4d76f73f11d9b95609dddac3717dbd7e *man/h5Prep.Rd
-73c480de6c10480475c89ec27c4b988a *man/h5Read.Rd
+734515a6178bc598a0348f01f820f304 *man/h5Read.Rd
 c0052eb84def831ed64408f2c40576a7 *man/h5ReadDataset.Rd
 4fbea9b7744d9241d9fef19df2ffbc41 *man/h5TryOpen.Rd
 23d1d84660aea5b80a04f30d5c6147c0 *man/h5Write.Rd

diff --git a/NAMESPACE b/NAMESPACE
@@ -99,6 +99,7 @@ export(h5WriteDataset)
 export(h5WriteScalar)
 export(is.H5D)
 export(is.H5Group)
+importClassesFrom(Matrix,dgCMatrix)
 importClassesFrom(Matrix,dgRMatrix)
 importFrom(Matrix,sparseMatrix)
 importFrom(MatrixExtra,t_shallow)
@@ -116,7 +117,6 @@ importFrom(hdf5r,guess_chunks)
 importFrom(hdf5r,guess_dtype)
 importFrom(hdf5r,h5attr_names)
 importFrom(hdf5r,h5const)
-importFrom(hdf5r,h5garbage_collect)
 importFrom(methods,is)
 importFrom(methods,slot)
 importFrom(rlang,.data)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,13 @@
+# hdf5r.Extra 0.0.3
+## Bug fixes
+* Fixed bugs caused by `h5Write` when transform an S4 object to list.
+
+## Improvement
+* Clarify usage of `toS4.func` for `h5Read`.
+
 # hdf5r.Extra 0.0.2
 ## Bug fixes
-* Fixed bugs caused by `H5Backup` in old R release platform.
+* Fixed bugs caused by `h5Backup` in old R release platform.
 * Fixed bugs caused by not using `tempfile` in examples.
 
 ## Improvement

diff --git a/R/hdf5-functions.R b/R/hdf5-functions.R
@@ -27,6 +27,7 @@
 #' @export
 h5AbsLinkName <- function(name) {
   name <- name[1]
+  name <- gsub(pattern = "\\/*$", replacement = "", x = name)
   if (!any(isValidCharacters(x = name))) {
     name <- ""
   }
@@ -136,7 +137,7 @@ h5TryOpen <- function(
       if (!do.retry) {
         stop(e)
       }
-      message("Keep retrying per minute with 'timeout' set to ", timeout, " s")
+      message("Keep retrying per minute with 'timeout': ", timeout, " s")
       time <- 0
       while(time < timeout) {
         Sys.sleep(time = interval)
@@ -149,7 +150,10 @@ h5TryOpen <- function(
         }
         time <- time + interval
       }
-      stop("Reach a timeout after ", time, " s. Cannot open '", filename, "'")
+      stop(
+        "Reach a timeout after ", time, " s. ", 
+        "Cannot open '", filename, "': \n", e
+      )
     }
   ))
 }
@@ -359,13 +363,13 @@ h5Move <- function(
   h5fh <- h5TryOpen(filename = file, mode = "r+")
   on.exit(expr = h5fh$close())
   if (!h5Exists(x = h5fh, name = from.name)) {
-    stop("Cannot move a non-existing object: ", from.name)
+    stop("Source object doesn't exist: ", from.name)
   }
   if (h5Exists(x = h5fh, name = to.name)) {
     if (!overwrite) {
       warning(
-        "Destination object already exists. ",
-        "Set 'overwrite = TRUE' to remove it.",
+        "Destination object already exists: ", to.name,
+        "\nSet 'overwrite = TRUE' to remove it.",
         immediate. = TRUE
       )
       return(invisible(x = NULL))
@@ -375,8 +379,8 @@ h5Move <- function(
     }
     h5fh$link_delete(name = to.name)
   }
-  h5CreateGroup(
-    x = h5fh, 
+  .h5group_create_group(
+    h5group = h5fh, 
     name = dirname(path = to.name), 
     show.warnings = FALSE
   )
@@ -441,10 +445,10 @@ h5Backup <- function(
     )
   }
   if (identical(x = from.file, y = to.file)) {
-    stop("\n  The source file and the target file are identical.")
+    stop("\nThe source file and the target file are identical.")
   }
   if (!overwrite && file.exists(to.file)) {
-    stop("The destination file exists, please set 'overwrite = TRUE'")
+    stop("\nThe destination file exists, please set 'overwrite = TRUE'")
   }
   h5fh <- h5TryOpen(filename = from.file, mode = "r")
   all_links <- h5List(
@@ -463,7 +467,7 @@ h5Backup <- function(
     file.copy(from = from.file, to = to.file, overwrite = TRUE)
     return(to.file)
   }
-  on.exit(expr = h5fh$close())
+  on.exit(expr = h5fh$close(), add = TRUE)
   all_links <- all_links[all_links$name %in% keep_links, , drop = FALSE]
 
   to.h5fh <- h5TryOpen(filename = to.file, mode = "w")
@@ -558,7 +562,7 @@ h5Overwrite <- function(file, name, overwrite) {
       immediate. = TRUE
     )
     h5fh <- h5TryOpen(filename = file, mode = "w")
-    on.exit(expr = h5fh$close())
+    h5fh$close()
     return(file)
   }
   if (!h5Exists(x = file, name = name)) {
@@ -578,20 +582,19 @@ h5Overwrite <- function(file, name, overwrite) {
     "\n  File: ", file,
     "\n  Object: ", name
   )
-  file.rename(from = file, to = tmp.file)
   tryCatch(
     expr = {
       h5Backup(
-        from.file = tmp.file, 
-        to.file = file, 
+        from.file = file, 
+        to.file = tmp.file, 
         exclude = name, 
         overwrite = TRUE,
         verbose = FALSE
       )
-      unlink(x = tmp.file)
+      file.rename(from = tmp.file, to = file)
     },
     error = function(e) {
-      file.rename(from = tmp.file, to = file)
+      unlink(x = tmp.file)
       stop(e)
     }
   )