coFAST
Spatially-Aware Cell Clustering Algorithm with Cluster Significant Assessment
v0.2.0
·
Dec 13, 2025
·
GPL-3
Description
A spatially-aware cell clustering algorithm is provided with cluster significance assessment. It comprises four key modules: spatially-aware cell-gene co-embedding, cell clustering, signature gene identification, and cluster significant assessment. More details can be referred to Peng Xie, et al. (2025) <doi:10.1016/j.cell.2025.05.035>.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (3 non-OK)
NOTE
r-oldrel-macos-arm64
package dependencies
Package suggested but not available for checking: ‘scater’
ERROR
r-oldrel-macos-arm64
whether package can be installed
Installation failed. See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/coFAST.Rcheck/00install.out’ for details.
ERROR
r-release-macos-arm64
examples
Running examples in ‘coFAST-Ex.R’ failed The error most likely occurred in: > ### Name: diagnostic.cor.eigs > ### Title: Determine the dimension of low dimensional embedding > ### Aliases: diagnostic.cor.eigs diagnostic.cor.eigs.default > ### diagnostic.cor.eigs.Seurat > > ### ** Examples > > n <- 100 > p <- 50 > d <- 15 > object <- matrix(rnorm(n*d), n, d) %*% matrix(rnorm(d*p), d, p) > diagnostic.cor.eigs(object, n.sims=2) Warning in diagnostic.cor.eigs.default(object, n.sims = 2) : q_max is not less than the number of columns of X. Set it as ncol(X) - 1 Warning in irlba::irlba(A = Y/sqrt(n), nv = q_max) : You're computing too large a percentage of total singular values, use a standard svd instead. Progress: ──────────────────────────────────────────────────────────────── 100% *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: irlba::irlba(A = X1/sqrt(n), nv = q_max) 2: . ...[truncated]... = "map", env_globals = .env_globals) 60: furrr::future_map(1:n.sims, corr_fun, n = n, p = p, .progress = TRUE, .options = furrr::furrr_options(seed = seed)) 61: progress = .progress, type = "list", purrr_fn_name = "map", env_globals = .env_globals) 60: furrr::future_map(1:n.sims, corr_fun, n = n, p = p, .progress = TRUE, .options = furrr::furrr_options(seed = seed)) 61: diagnostic.cor.eigs.default(object, n.sims = 2)diagnostic.cor.eigs.default(object, n.sims = 2) 62: diagnostic.cor.eigs(object, n.sims = 2) 62: diagnostic.cor.eigs(object, n.sims = 2) An irrecoverable exception occurred. R is aborting now ... An irrecoverable exception occurred. R is aborting now ... Warning in file(file, open = "r") : cannot open file '/Volumes/Temp/tmp/RtmpVtOrBv/filee7b57d9208b0.txt': No such file or directory Error in file(file, open = "r") : cannot open the connection Calls: diagnostic.cor.eigs ... furrr_map_template -> furrr_template -> poll_progress -> file Execution halted
Check History
ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-devel-macos-arm64
package dependencies
Package required but not available: ‘ProFAST’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
ERROR
r-release-macos-arm64
examples
Running examples in ‘coFAST-Ex.R’ failed The error most likely occurred in: > ### Name: diagnostic.cor.eigs > ### Title: Determine the dimension of low dimensional embedding > ### Aliases: diagnostic.cor.eigs diagnostic.cor.eigs.default > ### diag ...[truncated]... 2>) of class MulticoreFuture was interrupted, while running on localhost (pid 73002) [future <unnamed-2> (30561e877663b5105e3b175a2a88ecee-2); on 30561e877663b5105e3b175a2a88ecee@macos13-vm.local<72998> at 2026-03-11 03:44:51.021652] Execution halted
ERROR
r-oldrel-macos-arm64
package dependencies
Package suggested but not available for checking: ‘scater’