Last updated on 2022-01-20 19:50:50 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | OK | ||||
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 23.53 | 92.25 | 115.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 211.35 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 175.68 | OK | |||
| r-devel-windows-x86_64-new-UL | 0.1.1 | 122.00 | 168.00 | 290.00 | OK | |
| r-devel-windows-x86_64-new-TK | 0.1.1 | OK | ||||
| r-patched-linux-x86_64 | 0.1.1 | 24.07 | 121.53 | 145.60 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 25.99 | 121.72 | 147.71 | OK | |
| r-release-macos-arm64 | 0.1.1 | OK | ||||
| r-release-macos-x86_64 | 0.1.1 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.1.1 | 75.00 | 205.00 | 280.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.1.1 | 75.00 | 162.00 | 237.00 | ERROR |
Version: 0.1.1
Check: running examples for arch ‘i386’
Result: ERROR
Running examples in 'ClustAssess-Ex.R' failed
The error most likely occurred in:
> ### Name: marker_overlap
> ### Title: Cell-wise marker gene overlap
> ### Aliases: marker_overlap
>
> ### ** Examples
>
> suppressWarnings({
+ set.seed(12345)
+ library(Seurat)
+
+ # cluster with Louvain algorithm
+ pbmc_small = FindClusters(pbmc_small, resolution=0.8, verbose=FALSE)
+
+ # cluster with k-means
+ pbmc.pca = Embeddings(pbmc_small, 'pca')
+ pbmc_small@meta.data$kmeans_clusters = kmeans(pbmc.pca, centers=2)$cluster
+
+ # compare the markers
+ Idents(pbmc_small) = pbmc_small@meta.data$seurat_clusters
+ louvain.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+
+ Idents(pbmc_small) = pbmc_small@meta.data$kmeans_clusters
+ kmeans.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+
+ pbmc_small@meta.data$jsi = marker_overlap(louvain.markers, kmeans.markers,
+ pbmc_small@meta.data$seurat_clusters, pbmc_small@meta.data$kmeans_clusters)
+
+ # which cells have the same markers, regardless of clustering?
+ FeaturePlot(pbmc_small, 'jsi')
+ })
Error: package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.1
Check: running examples for arch ‘x64’
Result: ERROR
Running examples in 'ClustAssess-Ex.R' failed
The error most likely occurred in:
> ### Name: marker_overlap
> ### Title: Cell-wise marker gene overlap
> ### Aliases: marker_overlap
>
> ### ** Examples
>
> suppressWarnings({
+ set.seed(12345)
+ library(Seurat)
+
+ # cluster with Louvain algorithm
+ pbmc_small = FindClusters(pbmc_small, resolution=0.8, verbose=FALSE)
+
+ # cluster with k-means
+ pbmc.pca = Embeddings(pbmc_small, 'pca')
+ pbmc_small@meta.data$kmeans_clusters = kmeans(pbmc.pca, centers=2)$cluster
+
+ # compare the markers
+ Idents(pbmc_small) = pbmc_small@meta.data$seurat_clusters
+ louvain.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+
+ Idents(pbmc_small) = pbmc_small@meta.data$kmeans_clusters
+ kmeans.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+
+ pbmc_small@meta.data$jsi = marker_overlap(louvain.markers, kmeans.markers,
+ pbmc_small@meta.data$seurat_clusters, pbmc_small@meta.data$kmeans_clusters)
+
+ # which cells have the same markers, regardless of clustering?
+ FeaturePlot(pbmc_small, 'jsi')
+ })
Error: package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'ClustAssess.Rmd' using rmarkdown
Quitting from lines 22-27 (ClustAssess.Rmd)
Error: processing vignette 'ClustAssess.Rmd' failed with diagnostics:
package or namespace load failed for 'Seurat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'Matrix' 1.3-2 is already loaded, but >= 1.3.3 is required
--- failed re-building 'ClustAssess.Rmd'
--- re-building 'comparing-soft-and-hierarchical.Rmd' using rmarkdown
--- finished re-building 'comparing-soft-and-hierarchical.Rmd'
SUMMARY: processing the following file failed:
'ClustAssess.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64