Merge pull request #95 from gagneurlab/DelayedSubset

gagneurlab · Feb 14, 2025 · baab0b2 · baab0b2
2 parents 3111d41 + b5d274f
commit baab0b2
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,10 +53,10 @@ jobs:
       matrix:
         config:
           # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. 
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'next', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:

diff --git a/R/saveHDF5Objects.R b/R/saveHDF5Objects.R
@@ -116,8 +116,16 @@ loadFraserDataSet <- function(dir, name=NULL, file=NULL, upgrade=FALSE){
             path(assay(fds, aname, withDimnames=FALSE)) <- afile
         } else if("DelayedMatrix" == 
                     class(assay(fds, aname, withDimnames=FALSE))){
-            slot(slot(slot(assay(fds, aname, withDimnames=FALSE), 
-                    "seed"), "seed"), "filepath") <- afile
+	    tryCatch(
+		{
+                    slot(slot(slot(assay(fds, aname, withDimnames=FALSE), 
+                        "seed"), "seed"), "filepath") <- afile
+	        },
+	        error = function(e) {
+		    slot(slot(slot(slot(assay(fds, aname, withDimnames = FALSE),
+                        "seed"), "seed"), "seed"), "filepath") <- afile
+	        }
+	    )   
         # if its a HDF5 matrix we have one seed less
         } else {
             slot(slot(assay(fds, aname, withDimnames=FALSE),