From dd2b3e189fc26fc0e574043c231c0b43eef2c41c Mon Sep 17 00:00:00 2001
From: LTLA Site built with pkgdown 2.1.0. Site built with pkgdown 2.1.1.Page not found (404)
diff --git a/LICENSE-text.html b/LICENSE-text.html
index f8cdb25..a7cebde 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -72,7 +72,7 @@ License
diff --git a/articles/index.html b/articles/index.html
index dfdf909..159f702 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -69,7 +69,7 @@ All vignettes
diff --git a/articles/userguide.html b/articles/userguide.html
index b42399f..93f8669 100644
--- a/articles/userguide.html
+++ b/articles/userguide.html
@@ -531,9 +531,9 @@ Session information## [4] BiocGenerics_0.51.1 BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
-## [1] jsonlite_1.8.8 crayon_1.5.3 compiler_4.4.1
+## [1] jsonlite_1.8.9 crayon_1.5.3 compiler_4.4.1
## [4] BiocManager_1.30.25 Rcpp_1.0.13 rhdf5filters_1.17.0
-## [7] alabaster.matrix_1.5.8 jquerylib_0.1.4 systemfonts_1.1.0
+## [7] alabaster.matrix_1.5.9 jquerylib_0.1.4 systemfonts_1.1.0
## [10] IRanges_2.39.2 textshaping_0.4.0 yaml_2.3.10
## [13] fastmap_1.2.0 lattice_0.22-6 XVector_0.45.0
## [16] R6_2.5.1 S4Arrays_1.5.7 knitr_1.48
@@ -541,11 +541,11 @@
Session information## [22] desc_1.4.3 MatrixGenerics_1.17.0 bslib_0.8.0
## [25] rlang_1.1.4 HDF5Array_1.33.6 cachem_1.1.0
## [28] xfun_0.47 fs_1.6.4 sass_0.4.9
-## [31] SparseArray_1.5.31 cli_3.6.3 pkgdown_2.1.0
+## [31] SparseArray_1.5.37 cli_3.6.3 pkgdown_2.1.1
## [34] Rhdf5lib_1.27.0 zlibbioc_1.51.1 digest_0.6.37
## [37] grid_4.4.1 alabaster.schemas_1.5.0 rhdf5_2.49.0
-## [40] lifecycle_1.0.4 evaluate_0.24.0 ragg_1.3.2
-## [43] abind_1.4-5 rmarkdown_2.28 matrixStats_1.4.1
+## [40] lifecycle_1.0.4 evaluate_0.24.0 ragg_1.3.3
+## [43] abind_1.4-8 rmarkdown_2.28 matrixStats_1.4.1
## [46] tools_4.4.1 htmltools_0.5.8.1
@@ -565,7 +565,7 @@
Session information
-
Citation
diff --git a/index.html b/index.html
index da2bdd0..c1eb10a 100644
--- a/index.html
+++ b/index.html
@@ -288,7 +288,7 @@ Developers
diff --git a/pkgdown.yml b/pkgdown.yml
index ca18e6e..e50f733 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,6 @@
pandoc: 3.1.11
-pkgdown: 2.1.0
+pkgdown: 2.1.1
pkgdown_sha: ~
articles:
userguide: userguide.html
-last_built: 2024-09-13T17:00Z
+last_built: 2024-09-22T19:42Z
diff --git a/reference/Rfc3339.html b/reference/Rfc3339.html
index c0216be..59e087e 100644
--- a/reference/Rfc3339.html
+++ b/reference/Rfc3339.html
@@ -163,46 +163,46 @@ Author
Examples
out <- as.Rfc3339(Sys.time() + 1:10)
out
-#> [1] "2024-09-13T17:00:12+00:00" "2024-09-13T17:00:13+00:00"
-#> [3] "2024-09-13T17:00:14+00:00" "2024-09-13T17:00:15+00:00"
-#> [5] "2024-09-13T17:00:16+00:00" "2024-09-13T17:00:17+00:00"
-#> [7] "2024-09-13T17:00:18+00:00" "2024-09-13T17:00:19+00:00"
-#> [9] "2024-09-13T17:00:20+00:00" "2024-09-13T17:00:21+00:00"
+#> [1] "2024-09-22T19:42:31+00:00" "2024-09-22T19:42:32+00:00"
+#> [3] "2024-09-22T19:42:33+00:00" "2024-09-22T19:42:34+00:00"
+#> [5] "2024-09-22T19:42:35+00:00" "2024-09-22T19:42:36+00:00"
+#> [7] "2024-09-22T19:42:37+00:00" "2024-09-22T19:42:38+00:00"
+#> [9] "2024-09-22T19:42:39+00:00" "2024-09-22T19:42:40+00:00"
#> attr(,"class")
#> [1] "Rfc3339"
out[2:5]
-#> [1] "2024-09-13T17:00:13+00:00" "2024-09-13T17:00:14+00:00"
-#> [3] "2024-09-13T17:00:15+00:00" "2024-09-13T17:00:16+00:00"
+#> [1] "2024-09-22T19:42:32+00:00" "2024-09-22T19:42:33+00:00"
+#> [3] "2024-09-22T19:42:34+00:00" "2024-09-22T19:42:35+00:00"
#> attr(,"class")
#> [1] "Rfc3339"
out[2] <- "2"
c(out, out)
-#> [1] "2024-09-13T17:00:12+00:00" NA
-#> [3] "2024-09-13T17:00:14+00:00" "2024-09-13T17:00:15+00:00"
-#> [5] "2024-09-13T17:00:16+00:00" "2024-09-13T17:00:17+00:00"
-#> [7] "2024-09-13T17:00:18+00:00" "2024-09-13T17:00:19+00:00"
-#> [9] "2024-09-13T17:00:20+00:00" "2024-09-13T17:00:21+00:00"
-#> [11] "2024-09-13T17:00:12+00:00" NA
-#> [13] "2024-09-13T17:00:14+00:00" "2024-09-13T17:00:15+00:00"
-#> [15] "2024-09-13T17:00:16+00:00" "2024-09-13T17:00:17+00:00"
-#> [17] "2024-09-13T17:00:18+00:00" "2024-09-13T17:00:19+00:00"
-#> [19] "2024-09-13T17:00:20+00:00" "2024-09-13T17:00:21+00:00"
+#> [1] "2024-09-22T19:42:31+00:00" NA
+#> [3] "2024-09-22T19:42:33+00:00" "2024-09-22T19:42:34+00:00"
+#> [5] "2024-09-22T19:42:35+00:00" "2024-09-22T19:42:36+00:00"
+#> [7] "2024-09-22T19:42:37+00:00" "2024-09-22T19:42:38+00:00"
+#> [9] "2024-09-22T19:42:39+00:00" "2024-09-22T19:42:40+00:00"
+#> [11] "2024-09-22T19:42:31+00:00" NA
+#> [13] "2024-09-22T19:42:33+00:00" "2024-09-22T19:42:34+00:00"
+#> [15] "2024-09-22T19:42:35+00:00" "2024-09-22T19:42:36+00:00"
+#> [17] "2024-09-22T19:42:37+00:00" "2024-09-22T19:42:38+00:00"
+#> [19] "2024-09-22T19:42:39+00:00" "2024-09-22T19:42:40+00:00"
#> attr(,"class")
#> [1] "Rfc3339"
as.character(out)
-#> [1] "2024-09-13T17:00:12+00:00" NA
-#> [3] "2024-09-13T17:00:14+00:00" "2024-09-13T17:00:15+00:00"
-#> [5] "2024-09-13T17:00:16+00:00" "2024-09-13T17:00:17+00:00"
-#> [7] "2024-09-13T17:00:18+00:00" "2024-09-13T17:00:19+00:00"
-#> [9] "2024-09-13T17:00:20+00:00" "2024-09-13T17:00:21+00:00"
+#> [1] "2024-09-22T19:42:31+00:00" NA
+#> [3] "2024-09-22T19:42:33+00:00" "2024-09-22T19:42:34+00:00"
+#> [5] "2024-09-22T19:42:35+00:00" "2024-09-22T19:42:36+00:00"
+#> [7] "2024-09-22T19:42:37+00:00" "2024-09-22T19:42:38+00:00"
+#> [9] "2024-09-22T19:42:39+00:00" "2024-09-22T19:42:40+00:00"
as.POSIXct(out)
-#> [1] "2024-09-13 17:00:12 UTC" NA
-#> [3] "2024-09-13 17:00:14 UTC" "2024-09-13 17:00:15 UTC"
-#> [5] "2024-09-13 17:00:16 UTC" "2024-09-13 17:00:17 UTC"
-#> [7] "2024-09-13 17:00:18 UTC" "2024-09-13 17:00:19 UTC"
-#> [9] "2024-09-13 17:00:20 UTC" "2024-09-13 17:00:21 UTC"
+#> [1] "2024-09-22 19:42:31 UTC" NA
+#> [3] "2024-09-22 19:42:33 UTC" "2024-09-22 19:42:34 UTC"
+#> [5] "2024-09-22 19:42:35 UTC" "2024-09-22 19:42:36 UTC"
+#> [7] "2024-09-22 19:42:37 UTC" "2024-09-22 19:42:38 UTC"
+#> [9] "2024-09-22 19:42:39 UTC" "2024-09-22 19:42:40 UTC"
Examples
diff --git a/reference/acquireFile.html b/reference/acquireFile.html
index 38e70d0..3bca621 100644
--- a/reference/acquireFile.html
+++ b/reference/acquireFile.html
@@ -184,7 +184,7 @@ Examples
# Retrieving the file:
acquireFile(tmp, "coldata/simple.csv.gz")
-#> [1] "/tmp/Rtmpftsb5q/file2c87c9db4cb/coldata/simple.csv.gz"
+#> [1] "/tmp/Rtmpr7csNv/file7e987c7925/coldata/simple.csv.gz"
@@ -200,7 +200,7 @@ Examples
diff --git a/reference/altReadObject.html b/reference/altReadObject.html
index 049f400..73cc022 100644
--- a/reference/altReadObject.html
+++ b/reference/altReadObject.html
@@ -162,7 +162,7 @@ Examples
diff --git a/reference/altSaveObject.html b/reference/altSaveObject.html
index 3d31034..7877432 100644
--- a/reference/altSaveObject.html
+++ b/reference/altSaveObject.html
@@ -151,7 +151,7 @@ Examples
diff --git a/reference/anyMissing.html b/reference/anyMissing.html
index 0b10187..4621a97 100644
--- a/reference/anyMissing.html
+++ b/reference/anyMissing.html
@@ -116,7 +116,7 @@ Examples
diff --git a/reference/chooseMissingPlaceholderForHdf5.html b/reference/chooseMissingPlaceholderForHdf5.html
index d7c3d1b..fd8ee85 100644
--- a/reference/chooseMissingPlaceholderForHdf5.html
+++ b/reference/chooseMissingPlaceholderForHdf5.html
@@ -119,7 +119,7 @@ Examples
diff --git a/reference/createRedirection.html b/reference/createRedirection.html
index c54e8f5..65a9f8b 100644
--- a/reference/createRedirection.html
+++ b/reference/createRedirection.html
@@ -167,7 +167,7 @@ Examples
diff --git a/reference/hdf5.html b/reference/hdf5.html
index 23522fa..0842e3d 100644
--- a/reference/hdf5.html
+++ b/reference/hdf5.html
@@ -75,7 +75,7 @@ HDF5 utilities
diff --git a/reference/index.html b/reference/index.html
index 3f7cd63..e35f367 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -101,6 +101,10 @@ All functions
moveObject()
Move a non-child object in the staging directory
collect_integer_attributes()
optimize_integer_storage()
collect_number_attributes()
optimize_number_storage()
collect_string_attributes()
optimize_string_storage()
collect_boolean_attributes()
optimize_boolean_storage()
HDF5 storage type optimization
Optimize HDF5 storage to use the smallest possible storage type. +Intended for alabaster.* developers only.
+collect_integer_attributes(x)
+
+optimize_integer_storage(x)
+
+collect_number_attributes(x)
+
+optimize_number_storage(x, fallback = chooseMissingPlaceholderForHdf5)
+
+collect_string_attributes(x)
+
+optimize_string_storage(x, fallback = NULL)
+
+collect_boolean_attributes(x)
+
+optimize_boolean_storage(x)
An atomic vector or array of the specified type,
+e.g., integer vector/array for collect_integer_attributes
and optimize_integer_storage
.
+Developers can also extend this to abstract objects containing values of the same type, e.g., matrix-like S4 classes.
Function that accepts x
and returns a suitable placeholder in the presence of NA
s.
+If NULL
, this defaults to chooseMissingPlaceholderForHdf5
.
For collect_integer_attributes
, a named list containing:
min
, the smallest non-NA
value in x
.
+This is set to Inf if all values are NA
.
max
, the largest non-NA
value in x
.
+This is set to -Inf if all values are NA
.
missing
, logical scalar indicating whether any values in x
are NA
.
For collect_number_attributes
, a named list containing:
missing
, logical scalar indicating whether any values in x
are NA
.
non_integer
, logical scalar indicating whether any values in x
are non-integer.
min
, the smallest non-NA
integer value in x
.
+This is set to Inf if there are any non-integer or NA
values.
max
, the largest non-NA
integer value in x
.
+This is set to -Inf if there are any non-integer or NA
values.
has_NaN
, logical scalar indicating whether NaN is present in x
.
has_Inf
, logical scalar indicating whether positive infinity is present in x
.
has_NegInf
, logical scalar indicating whether negative infinity is present in x
.
has_lowest
, logical scalar indicating whether the smallest double-precision value is present in x
.
has_highest
, logical scalar indicating whether the highest double-precision value is present in x
.
For collect_string_attributes
, a named list containing:
missing
, logical scalar indicating whether any values in x
are NA
.
has_NA
, logical scalar indicating whether the "NA"
string is present in x
.
has__NA
, logical scalar indicating whether the "_NA"
string is present in x
.
max_len
, integer scalar specifying the maximum length of the strings in x
.
For collect_boolean_attributes
, a named list containing:
missing
, logical scalar indicating whether any values in x
are NA
.
For the optimize_*_storage
functions, a named list containing:
type
, string containing the HDF5 datatype for storing x
.
placeholder
, value of the placeholder for NA
values.
other
, other attributes of x
(e.g., number of non-zero elements for sparse vectors).
+These should be stored in an other
field in the named list returned by collect_*_ attributes
.