HenrikBengtsson commented 2 years ago

Hi. There's a missing dependency (Imports or Suggests) on DelayedMatrixStats in this package;

data('slingshotExample', package = "slingshot")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
condition <- factor(rep(c('A','B'), length.out = nrow(rd)))
condition[110:139] <- 'A'
sds <- slingshot::slingshot(rd, cl)
#> Error in loadNamespace(x) : 
#> there is no package called ‘DelayedMatrixStats’

> traceback()
20: stop(cond)
19: doWithOneRestart(return(expr), restart)
18: withOneRestart(expr, restarts[[1L]])
17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
16: loadNamespace(x)
15: .rowstats_w(DelayedArray::DelayedArray(x), group, FUN = DelayedMatrixStats::colWeightedMeans)
14: FUN(x, clusters)
13: .local(x, ...)
12: createClusterMST(x = X, clusters = clusterLabels, outgroup = omega, 
        outscale = omega_scale, endpoints = end.clus, dist.method = dist.method, 
        use.median = use.median, ...)
11: createClusterMST(x = X, clusters = clusterLabels, outgroup = omega, 
        outscale = omega_scale, endpoints = end.clus, dist.method = dist.method, 
        use.median = use.median, ...)
10: .local(data, clusterLabels, ...)
9: getLineages(data = data, clusterLabels = clusWeight, ...)
8: getLineages(data = data, clusterLabels = clusWeight, ...)
7: getLineages(data, clusterLabels, reducedDim = reducedDim, start.clus = start.clus, 
       end.clus = end.clus, dist.method = dist.method, use.median = use.median, 
       omega = omega, omega_scale = omega_scale, times = times)
6: getLineages(data, clusterLabels, reducedDim = reducedDim, start.clus = start.clus, 
       end.clus = end.clus, dist.method = dist.method, use.median = use.median, 
       omega = omega, omega_scale = omega_scale, times = times)
5: .local(data, clusterLabels, ...)
4: slingshot(data = data, clusterLabels = as.character(clusterLabels), 
       ...)
3: slingshot(data = data, clusterLabels = as.character(clusterLabels), 
       ...)
2: slingshot::slingshot(rd, cl)
1: slingshot::slingshot(rd, cl)

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /software/c4/cbi/software/R-4.1.3-gcc8/lib64/R/lib/libRblas.so
LAPACK: /software/c4/cbi/software/R-4.1.3-gcc8/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=C              
 [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=C           LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C           
[10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3                igraph_1.2.11              
 [3] XVector_0.34.0              magrittr_2.0.2             
 [5] GenomicRanges_1.46.1        BiocGenerics_0.40.0        
 [7] zlibbioc_1.40.0             rappdirs_0.3.3             
 [9] IRanges_2.28.0              lattice_0.20-45            
[11] GenomeInfoDb_1.30.0         tools_4.1.3                
[13] SummarizedExperiment_1.24.0 grid_4.1.3                 
[15] Biobase_2.54.0              matrixStats_0.61.0-9003    
[17] crayon_1.5.0                Matrix_1.4-0               
[19] GenomeInfoDbData_1.2.7      TrajectoryUtils_1.2.0      
[21] S4Vectors_0.32.3            bitops_1.0-7               
[23] RCurl_1.98-1.6              SingleCellExperiment_1.16.0
[25] princurve_2.1.6             DelayedArray_0.20.0        
[27] compiler_4.1.3              MatrixGenerics_1.6.0       
[29] stats4_4.1.3                slingshot_2.2.0            
[31] pkgconfig_2.0.3

kstreet13 / slingshot

Error: there is no package called ‘DelayedMatrixStats’ #178

See also