Comments (3)
Hi,
thanks for reporting this, I thought I had solved that bug before though... you say version 1.1.8, but current version is 1.1.6 - can you double check that?
Pierre-Luc
from scdblfinder.
Thanks for the quick reply. Here is my package description from R 3.6.3 and bioconductor 3.10:
Package: scDblFinder
Type: Package
Title: scDblFinder
Version: 1.1.8
Depends: R (>= 3.6)
Authors@R: person("Pierre-Luc", "Germain", email="[email protected]", role=c("cre","aut"), comment=c(ORCID="0000-0003-3418-4218"))
URL: https://github.com/plger/scDblFinder
BugReports: https://github.com/plger/scDblFinder/issues
Description: Efficient identification of doublets in single-cell RNAseq directly from counts using overclustering-based generation of artifical doublets.
License: GPL-3
Imports: igraph, Matrix, matrixStats, BiocParallel, BiocNeighbors,
SummarizedExperiment, SingleCellExperiment, scran, scater,
data.table, dplyr, ggplot2, randomForest, graphics, methods,
stats, DelayedArray
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 6.1.1
biocViews: Preprocessing, SingleCell, RNASeq
git_url: https://git.bioconductor.org/packages/scDblFinder
git_branch: RELEASE_3_10
git_last_commit: f9806b7
git_last_commit_date: 2020-03-05
Date/Publication: 2020-03-05
NeedsCompilation: no
Packaged: 2020-03-06 06:51:06 UTC; biocbuild
Author: Pierre-Luc Germain [cre, aut] (https://orcid.org/0000-0003-3418-4218)
Maintainer: Pierre-Luc Germain [email protected]
Built: R 3.6.3; ; 2020-03-06 13:43:44 UTC; windows
I tried to re-install after receiving your reply. When I tried to use R 4.0.0 and bioconductor 3.11 to install the devel version of it, the version was 1.1.6. When I tried to use R 3.6.3 and bioconductor 3.10 to install, the version was still 1.1.8. Devtools installation of scDblFinder returns V 1.1.6 for now.
I tired running this step again in V 1.1.6 and it worked well. V 1.1.8 still caused this error. I remember I gave up the 1.1.6 version and choose the 1.1.8 version before.
from scdblfinder.
Hi,
thanks for pointing out the inconsistency. It should disappear in the next daily build.
from scdblfinder.
Related Issues (20)
- Running scDblFinder deterministic and serial with the 'samples' parameter HOT 3
- Error in installing scDblFinder: object ‘colBlockApply’ is not exported by 'namespace:beachmat' HOT 5
- How to find all features used in training HOT 1
- Doublet numbers still not reproduced even though I used BPPARAM and bpstart HOT 2
- Deprecated "dgcMatrix" HOT 2
- scDbliFinder.sample is different from the sample column specified in `scDblFinder` function `samples` column ? HOT 17
- doublets mostly differ between scDblFinder and doubletFinder HOT 18
- Merging multiple samples with scATAC prior to scDblFinder HOT 2
- Unreasonably high doublets rate HOT 6
- scDblFinder - known doublets HOT 6
- Return threshold in output? HOT 4
- Installing scDblFinder with conda not working HOT 6
- error in serialize(data) HOT 6
- I'm having an issues with sctransform not sure HOT 1
- did not converge HOT 5
- Filter ATAC before running scDblFinder HOT 2
- Error when running library(scDblFinder) on jupyter through %%R HOT 2
- Error in if (length(expected) > 1 && x > min(expected) && x < max(expected)) return(0): missing value where TRUE/FALSE needed HOT 9
- Runing scDblFinder before and after removing low QC cells gives different results HOT 1
- Request for clarification of dbr and dbr.sd in scDblFinder 1.15.1 HOT 4
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