Revert "renku run: committing 4 newly added files"

This reverts commit 58a39885

log/process_cellbench.Rout

@@ -222,90 +222,9 @@ clusters
 > ## Save normalized counts as gziped mtx file
 > mtx <- as.matrix(logcounts(sce))
 > mtx <- Matrix(mtx)
-> mtx <- as(mtx, "dgTMatrix")
 > matrix_out <- paste0(out_path, "/norm_counts_", dataset_name, ".mtx")
 > writeMM(obj = mtx, matrix_out)
-NULL
-> gzip(matrix_out, overwrite=TRUE)
-> 
-> 
-> 
-> ## Save reduced Dimensions as gziped mtx
-> colnames(reducedDims(sce)[["UMAP"]]) <- c("UMAP1", "UMAP2")
-> red_tab <- cbind(reducedDims(sce)[["PCA"]], reducedDims(sce)[["UMAP"]])
-> red_mtx <- as.matrix(red_tab)
-> red_mtx <- Matrix(red_mtx)
-> red_mtx <- as(red_mtx, "dgTMatrix")
-> red_out <- paste0(out_path, "/dim_red", dataset_name, ".mtx")
-> writeMM(obj = red_mtx, red_out)
-NULL
-> gzip(red_out, overwrite=TRUE)
-> 
-> 
-> ## Save highly variable genes as json
-> jsonlite::write_json(hvg_tab, paste0(out_path, "/hvg_", dataset_name, ".json"), 
-+                      matrix = "columnmajor")
-> 
-> sessionInfo()
-R version 4.0.4 (2021-02-15)
-Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Ubuntu 20.04 LTS
-
-Matrix products: default
-BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
-
-locale:
- [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
- [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
- [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
- [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
- [9] LC_ADDRESS=C               LC_TELEPHONE=C            
-[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
-
-attached base packages:
-[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
-[8] methods   base     
-
-other attached packages:
- [1] uwot_0.1.8                  jsonlite_1.6.1             
- [3] Matrix_1.2-18               R.utils_2.9.2              
- [5] R.oo_1.23.0                 R.methodsS3_1.8.0          
- [7] scran_1.18.7                scater_1.18.6              
- [9] ggplot2_3.3.0               SingleCellExperiment_1.12.0
-[11] SummarizedExperiment_1.20.0 Biobase_2.50.0             
-[13] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
-[15] IRanges_2.24.1              S4Vectors_0.28.1           
-[17] BiocGenerics_0.36.1         MatrixGenerics_1.2.1       
-[19] matrixStats_0.58.0         
-
-loaded via a namespace (and not attached):
- [1] Rcpp_1.0.4                rsvd_1.0.3               
- [3] locfit_1.5-9.4            lattice_0.20-41          
- [5] FNN_1.1.3                 assertthat_0.2.1         
- [7] R6_2.4.1                  bluster_1.0.0            
- [9] pillar_1.4.3              sparseMatrixStats_1.2.1  
-[11] zlibbioc_1.36.0           rlang_0.4.5              
-[13] irlba_2.3.3               BiocNeighbors_1.8.2      
-[15] BiocParallel_1.24.1       statmod_1.4.34           
-[17] igraph_1.2.5              RCurl_1.98-1.1           
-[19] munsell_0.5.0             beachmat_2.6.4           
-[21] DelayedArray_0.16.3       compiler_4.0.4           
-[23] vipor_0.4.5               BiocSingular_1.6.0       
-[25] pkgconfig_2.0.3           ggbeeswarm_0.6.0         
-[27] tidyselect_1.0.0          tibble_2.1.3             
-[29] gridExtra_2.3             GenomeInfoDbData_1.2.4   
-[31] edgeR_3.32.1              viridisLite_0.3.0        
-[33] crayon_1.3.4              dplyr_0.8.5              
-[35] withr_2.1.2               bitops_1.0-6             
-[37] grid_4.0.4                gtable_0.3.0             
-[39] lifecycle_0.2.0           magrittr_1.5             
-[41] scales_1.1.0              dqrng_0.2.1              
-[43] scuttle_1.0.4             XVector_0.30.0           
-[45] viridis_0.5.1             limma_3.46.0             
-[47] DelayedMatrixStats_1.12.3 tools_4.0.4              
-[49] glue_1.3.2                beeswarm_0.2.3           
-[51] purrr_0.3.3               colorspace_1.4-1         
-> 
-> proc.time()
-   user  system elapsed 
-435.451 213.758 306.524 
+Error in (function (classes, fdef, mtable)  : 
+  unable to find an inherited method for function ‘writeMM’ for signature ‘"dgeMatrix"’
+Calls: writeMM -> <Anonymous>
+Execution halted