From b34223e8048c5591aafb090a38743ca2b03a912c Mon Sep 17 00:00:00 2001 From: LTLA Date: Sat, 9 Nov 2024 09:40:07 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Artifact?= =?UTF-8?q?DB/alabaster.base@f0bce72bf51360c63e43842d123b03d6f5dd3f61=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/index.html | 2 +- articles/userguide.html | 28 +++++----- authors.html | 6 +- index.html | 2 +- pkgdown.yml | 2 +- reference/Rfc3339.html | 56 +++++++++---------- reference/acquireFile.html | 4 +- reference/altReadObject.html | 2 +- reference/altSaveObject.html | 2 +- reference/anyMissing.html | 2 +- .../chooseMissingPlaceholderForHdf5.html | 2 +- reference/createRedirection.html | 2 +- reference/hdf5.html | 2 +- reference/index.html | 2 +- reference/listObjects.html | 2 +- reference/loadDirectory.html | 2 +- reference/moveObject.html | 2 +- reference/quickLoadObject.html | 2 +- reference/quickReadCsv.html | 2 +- reference/readAtomicVector.html | 2 +- reference/readBaseFactor.html | 2 +- reference/readBaseList.html | 2 +- reference/readDataFrame.html | 2 +- reference/readDataFrameFactor.html | 2 +- reference/readMetadata.html | 2 +- reference/readObject.html | 2 +- reference/readObjectFile.html | 2 +- reference/removeObject.html | 2 +- reference/saveAtomicVector.html | 2 +- reference/saveBaseFactor.html | 2 +- reference/saveBaseList.html | 2 +- reference/saveDataFrameFactor.html | 2 +- reference/saveFormats.html | 2 +- reference/saveMetadata.html | 2 +- reference/saveObject.html | 2 +- reference/stageDataFrame.html | 2 +- reference/transformVectorForHdf5.html | 2 +- reference/validateDirectory.html | 4 +- reference/validateObject.html | 2 +- reference/writeMetadata.html | 2 +- 42 files changed, 86 insertions(+), 86 deletions(-) diff --git a/404.html b/404.html index accb34a..7122f18 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/LICENSE-text.html b/LICENSE-text.html index fc667a8..66a9622 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/articles/index.html b/articles/index.html index 4728af5..4dcf3f5 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/articles/userguide.html b/articles/userguide.html index da689db..be44a5c 100644 --- a/articles/userguide.html +++ b/articles/userguide.html @@ -32,7 +32,7 @@ alabaster.base - 1.5.10 + 1.7.1 @@ -527,23 +527,23 @@

Session information## [8] base ## ## other attached packages: -## [1] Matrix_1.7-0 alabaster.base_1.5.10 S4Vectors_0.43.2 -## [4] BiocGenerics_0.51.3 BiocStyle_2.33.1 +## [1] Matrix_1.7-1 alabaster.base_1.7.1 S4Vectors_0.44.0 +## [4] BiocGenerics_0.52.0 BiocStyle_2.34.0 ## ## loaded via a namespace (and not attached): ## [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_1.5.10 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_1.5.11 knitr_1.48 -## [19] htmlwidgets_1.6.4 DelayedArray_0.31.14 bookdown_0.41 -## [22] desc_1.4.3 MatrixGenerics_1.17.0 bslib_0.8.0 -## [25] rlang_1.1.4 HDF5Array_1.33.8 cachem_1.1.0 +## [4] BiocManager_1.30.25 Rcpp_1.0.13 rhdf5filters_1.18.0 +## [7] alabaster.matrix_1.6.0 jquerylib_0.1.4 systemfonts_1.1.0 +## [10] IRanges_2.40.0 textshaping_0.4.0 yaml_2.3.10 +## [13] fastmap_1.2.0 lattice_0.22-6 XVector_0.46.0 +## [16] R6_2.5.1 S4Arrays_1.6.0 knitr_1.48 +## [19] htmlwidgets_1.6.4 DelayedArray_0.32.0 bookdown_0.41 +## [22] desc_1.4.3 MatrixGenerics_1.18.0 bslib_0.8.0 +## [25] rlang_1.1.4 HDF5Array_1.34.0 cachem_1.1.0 ## [28] xfun_0.48 fs_1.6.4 sass_0.4.9 -## [31] SparseArray_1.5.44 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 +## [31] SparseArray_1.6.0 cli_3.6.3 pkgdown_2.1.1 +## [34] Rhdf5lib_1.28.0 zlibbioc_1.52.0 digest_0.6.37 +## [37] grid_4.4.1 alabaster.schemas_1.6.0 rhdf5_2.50.0 ## [40] lifecycle_1.0.4 evaluate_1.0.1 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 diff --git a/authors.html b/authors.html index 9a0eb0f..ccf46bc 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 @@ -70,13 +70,13 @@

Citation

Lun A (2024). alabaster.base: Save Bioconductor Objects To File. -R package version 1.5.10, https://github.com/ArtifactDB/alabaster.base. +R package version 1.7.1, https://github.com/ArtifactDB/alabaster.base. 

@Manual{,
   title = {alabaster.base: Save Bioconductor Objects To File},
   author = {Aaron Lun},
   year = {2024},
-  note = {R package version 1.5.10},
+  note = {R package version 1.7.1},
   url = {https://github.com/ArtifactDB/alabaster.base},
 }
diff --git a/index.html b/index.html index e02c161..ed52cad 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/pkgdown.yml b/pkgdown.yml index 6715938..ca2d544 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: userguide: userguide.html -last_built: 2024-10-17T19:50Z +last_built: 2024-11-09T09:39Z diff --git a/reference/Rfc3339.html b/reference/Rfc3339.html index 704269e..73a3981 100644 --- a/reference/Rfc3339.html +++ b/reference/Rfc3339.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 @@ -163,46 +163,46 @@

Author

Examples

out <- as.Rfc3339(Sys.time() + 1:10)
 out
-#>  [1] "2024-10-17T19:50:45+00:00" "2024-10-17T19:50:46+00:00"
-#>  [3] "2024-10-17T19:50:47+00:00" "2024-10-17T19:50:48+00:00"
-#>  [5] "2024-10-17T19:50:49+00:00" "2024-10-17T19:50:50+00:00"
-#>  [7] "2024-10-17T19:50:51+00:00" "2024-10-17T19:50:52+00:00"
-#>  [9] "2024-10-17T19:50:53+00:00" "2024-10-17T19:50:54+00:00"
+#>  [1] "2024-11-09T09:39:49+00:00" "2024-11-09T09:39:50+00:00"
+#>  [3] "2024-11-09T09:39:51+00:00" "2024-11-09T09:39:52+00:00"
+#>  [5] "2024-11-09T09:39:53+00:00" "2024-11-09T09:39:54+00:00"
+#>  [7] "2024-11-09T09:39:55+00:00" "2024-11-09T09:39:56+00:00"
+#>  [9] "2024-11-09T09:39:57+00:00" "2024-11-09T09:39:58+00:00"
 #> attr(,"class")
 #> [1] "Rfc3339"
 
 out[2:5]
-#> [1] "2024-10-17T19:50:46+00:00" "2024-10-17T19:50:47+00:00"
-#> [3] "2024-10-17T19:50:48+00:00" "2024-10-17T19:50:49+00:00"
+#> [1] "2024-11-09T09:39:50+00:00" "2024-11-09T09:39:51+00:00"
+#> [3] "2024-11-09T09:39:52+00:00" "2024-11-09T09:39:53+00:00"
 #> attr(,"class")
 #> [1] "Rfc3339"
 out[2] <- "2"
 c(out, out)
-#>  [1] "2024-10-17T19:50:45+00:00" NA                         
-#>  [3] "2024-10-17T19:50:47+00:00" "2024-10-17T19:50:48+00:00"
-#>  [5] "2024-10-17T19:50:49+00:00" "2024-10-17T19:50:50+00:00"
-#>  [7] "2024-10-17T19:50:51+00:00" "2024-10-17T19:50:52+00:00"
-#>  [9] "2024-10-17T19:50:53+00:00" "2024-10-17T19:50:54+00:00"
-#> [11] "2024-10-17T19:50:45+00:00" NA                         
-#> [13] "2024-10-17T19:50:47+00:00" "2024-10-17T19:50:48+00:00"
-#> [15] "2024-10-17T19:50:49+00:00" "2024-10-17T19:50:50+00:00"
-#> [17] "2024-10-17T19:50:51+00:00" "2024-10-17T19:50:52+00:00"
-#> [19] "2024-10-17T19:50:53+00:00" "2024-10-17T19:50:54+00:00"
+#>  [1] "2024-11-09T09:39:49+00:00" NA                         
+#>  [3] "2024-11-09T09:39:51+00:00" "2024-11-09T09:39:52+00:00"
+#>  [5] "2024-11-09T09:39:53+00:00" "2024-11-09T09:39:54+00:00"
+#>  [7] "2024-11-09T09:39:55+00:00" "2024-11-09T09:39:56+00:00"
+#>  [9] "2024-11-09T09:39:57+00:00" "2024-11-09T09:39:58+00:00"
+#> [11] "2024-11-09T09:39:49+00:00" NA                         
+#> [13] "2024-11-09T09:39:51+00:00" "2024-11-09T09:39:52+00:00"
+#> [15] "2024-11-09T09:39:53+00:00" "2024-11-09T09:39:54+00:00"
+#> [17] "2024-11-09T09:39:55+00:00" "2024-11-09T09:39:56+00:00"
+#> [19] "2024-11-09T09:39:57+00:00" "2024-11-09T09:39:58+00:00"
 #> attr(,"class")
 #> [1] "Rfc3339"
 
 as.character(out)
-#>  [1] "2024-10-17T19:50:45+00:00" NA                         
-#>  [3] "2024-10-17T19:50:47+00:00" "2024-10-17T19:50:48+00:00"
-#>  [5] "2024-10-17T19:50:49+00:00" "2024-10-17T19:50:50+00:00"
-#>  [7] "2024-10-17T19:50:51+00:00" "2024-10-17T19:50:52+00:00"
-#>  [9] "2024-10-17T19:50:53+00:00" "2024-10-17T19:50:54+00:00"
+#>  [1] "2024-11-09T09:39:49+00:00" NA                         
+#>  [3] "2024-11-09T09:39:51+00:00" "2024-11-09T09:39:52+00:00"
+#>  [5] "2024-11-09T09:39:53+00:00" "2024-11-09T09:39:54+00:00"
+#>  [7] "2024-11-09T09:39:55+00:00" "2024-11-09T09:39:56+00:00"
+#>  [9] "2024-11-09T09:39:57+00:00" "2024-11-09T09:39:58+00:00"
 as.POSIXct(out)
-#>  [1] "2024-10-17 19:50:45 UTC" NA                       
-#>  [3] "2024-10-17 19:50:47 UTC" "2024-10-17 19:50:48 UTC"
-#>  [5] "2024-10-17 19:50:49 UTC" "2024-10-17 19:50:50 UTC"
-#>  [7] "2024-10-17 19:50:51 UTC" "2024-10-17 19:50:52 UTC"
-#>  [9] "2024-10-17 19:50:53 UTC" "2024-10-17 19:50:54 UTC"
+#>  [1] "2024-11-09 09:39:49 UTC" NA                       
+#>  [3] "2024-11-09 09:39:51 UTC" "2024-11-09 09:39:52 UTC"
+#>  [5] "2024-11-09 09:39:53 UTC" "2024-11-09 09:39:54 UTC"
+#>  [7] "2024-11-09 09:39:55 UTC" "2024-11-09 09:39:56 UTC"
+#>  [9] "2024-11-09 09:39:57 UTC" "2024-11-09 09:39:58 UTC"
diff --git a/reference/acquireFile.html b/reference/acquireFile.html index 0361af6..78564bd 100644 --- a/reference/acquireFile.html +++ b/reference/acquireFile.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.10 + 1.7.1 @@ -184,7 +184,7 @@

Examples

# Retrieving the file: acquireFile(tmp, "coldata/simple.csv.gz") -#> [1] "/tmp/RtmpZN8qnf/file7c041152aa3/coldata/simple.csv.gz" +#> [1] "/tmp/RtmpuX4xfq/file4dcd35dae283/coldata/simple.csv.gz" diff --git a/reference/altReadObject.html b/reference/altReadObject.html index 301a19a..4abcf9a 100644 --- a/reference/altReadObject.html +++ b/reference/altReadObject.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/altSaveObject.html b/reference/altSaveObject.html index 97072b1..1102d8a 100644 --- a/reference/altSaveObject.html +++ b/reference/altSaveObject.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/anyMissing.html b/reference/anyMissing.html index b34d98c..44f7e02 100644 --- a/reference/anyMissing.html +++ b/reference/anyMissing.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/chooseMissingPlaceholderForHdf5.html b/reference/chooseMissingPlaceholderForHdf5.html index 0bf1e60..8a98929 100644 --- a/reference/chooseMissingPlaceholderForHdf5.html +++ b/reference/chooseMissingPlaceholderForHdf5.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/createRedirection.html b/reference/createRedirection.html index 95c5a65..b911401 100644 --- a/reference/createRedirection.html +++ b/reference/createRedirection.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/hdf5.html b/reference/hdf5.html index cef520a..21ec34a 100644 --- a/reference/hdf5.html +++ b/reference/hdf5.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/index.html b/reference/index.html index c22ac25..7124638 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/listObjects.html b/reference/listObjects.html index 968f166..5ed9a08 100644 --- a/reference/listObjects.html +++ b/reference/listObjects.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/loadDirectory.html b/reference/loadDirectory.html index 5e89548..439e453 100644 --- a/reference/loadDirectory.html +++ b/reference/loadDirectory.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/moveObject.html b/reference/moveObject.html index f8b01c3..5f9c2ed 100644 --- a/reference/moveObject.html +++ b/reference/moveObject.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/quickLoadObject.html b/reference/quickLoadObject.html index f9d6429..5f16dcb 100644 --- a/reference/quickLoadObject.html +++ b/reference/quickLoadObject.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/quickReadCsv.html b/reference/quickReadCsv.html index e971b2b..c88db93 100644 --- a/reference/quickReadCsv.html +++ b/reference/quickReadCsv.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readAtomicVector.html b/reference/readAtomicVector.html index fb1a9ec..f2944d2 100644 --- a/reference/readAtomicVector.html +++ b/reference/readAtomicVector.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readBaseFactor.html b/reference/readBaseFactor.html index b543988..e171634 100644 --- a/reference/readBaseFactor.html +++ b/reference/readBaseFactor.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readBaseList.html b/reference/readBaseList.html index 2b26330..d0f2f30 100644 --- a/reference/readBaseList.html +++ b/reference/readBaseList.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readDataFrame.html b/reference/readDataFrame.html index f47ebaf..d637ae8 100644 --- a/reference/readDataFrame.html +++ b/reference/readDataFrame.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readDataFrameFactor.html b/reference/readDataFrameFactor.html index eba3c85..6a1aea6 100644 --- a/reference/readDataFrameFactor.html +++ b/reference/readDataFrameFactor.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readMetadata.html b/reference/readMetadata.html index 4e61a63..7013f29 100644 --- a/reference/readMetadata.html +++ b/reference/readMetadata.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readObject.html b/reference/readObject.html index e6972ab..25f8c5c 100644 --- a/reference/readObject.html +++ b/reference/readObject.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/readObjectFile.html b/reference/readObjectFile.html index a4a5cd4..04adc10 100644 --- a/reference/readObjectFile.html +++ b/reference/readObjectFile.html @@ -20,7 +20,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/removeObject.html b/reference/removeObject.html index 2f9e92a..5db26a1 100644 --- a/reference/removeObject.html +++ b/reference/removeObject.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveAtomicVector.html b/reference/saveAtomicVector.html index 2ce243d..b3e02d8 100644 --- a/reference/saveAtomicVector.html +++ b/reference/saveAtomicVector.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveBaseFactor.html b/reference/saveBaseFactor.html index 7d3b4cb..4c2b191 100644 --- a/reference/saveBaseFactor.html +++ b/reference/saveBaseFactor.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveBaseList.html b/reference/saveBaseList.html index 1f30a52..c7ecfa5 100644 --- a/reference/saveBaseList.html +++ b/reference/saveBaseList.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveDataFrameFactor.html b/reference/saveDataFrameFactor.html index b8077f8..f9ce407 100644 --- a/reference/saveDataFrameFactor.html +++ b/reference/saveDataFrameFactor.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveFormats.html b/reference/saveFormats.html index 2a67b78..dc1c10c 100644 --- a/reference/saveFormats.html +++ b/reference/saveFormats.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveMetadata.html b/reference/saveMetadata.html index bff07e3..a382393 100644 --- a/reference/saveMetadata.html +++ b/reference/saveMetadata.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/saveObject.html b/reference/saveObject.html index 8f1a584..6a3c653 100644 --- a/reference/saveObject.html +++ b/reference/saveObject.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/stageDataFrame.html b/reference/stageDataFrame.html index 8533fe4..6ce2c8d 100644 --- a/reference/stageDataFrame.html +++ b/reference/stageDataFrame.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/transformVectorForHdf5.html b/reference/transformVectorForHdf5.html index 176cf74..1a1a8cb 100644 --- a/reference/transformVectorForHdf5.html +++ b/reference/transformVectorForHdf5.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/validateDirectory.html b/reference/validateDirectory.html index 2628b77..605895d 100644 --- a/reference/validateDirectory.html +++ b/reference/validateDirectory.html @@ -17,7 +17,7 @@ alabaster.base - 1.5.10 + 1.7.1 @@ -119,7 +119,7 @@

Examples

write(file=file.path(tmp, "bar", "OBJECT"), '[ "WHEEE" ]') try(validateDirectory(tmp)) #> Error in value[[3L]](cond) : -#> failed to validate 'bar'; failed to read the OBJECT file at '/tmp/RtmpZN8qnf/file7c05a2525c8/bar'; metadata should be a JSON object +#> failed to validate 'bar'; failed to read the OBJECT file at '/tmp/RtmpuX4xfq/file4dcd7f99352/bar'; metadata should be a JSON object diff --git a/reference/validateObject.html b/reference/validateObject.html index 7a54788..e10a80f 100644 --- a/reference/validateObject.html +++ b/reference/validateObject.html @@ -18,7 +18,7 @@ alabaster.base - 1.5.10 + 1.7.1 diff --git a/reference/writeMetadata.html b/reference/writeMetadata.html index 93e02fb..5c9e882 100644 --- a/reference/writeMetadata.html +++ b/reference/writeMetadata.html @@ -19,7 +19,7 @@ alabaster.base - 1.5.10 + 1.7.1