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Delayedsubset fix #95

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merged 2 commits into from
Feb 14, 2025
Merged

Delayedsubset fix #95

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6bff84e
make loadFraserDataSet compatible with really old versions of FRASER
AtaJadidAhari Jan 15, 2025
b5d274f
Update bioc versions
AtaJadidAhari Jan 16, 2025
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8 changes: 4 additions & 4 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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12 changes: 10 additions & 2 deletions R/saveHDF5Objects.R
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Expand Up @@ -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),
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