Downloading GitHub repo rnabioco/clustifyrdata@master
✓  checking for file ‘/private/var/folders/fq/_zr6nbj12vlg13hz53xj2vgr0000gn/T/RtmpSyRqhZ/remotes163bb3b598210/rnabioco-clustifyrdata-8582364/DESCRIPTION’ ...
─  preparing ‘clustifyrdata’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
   /Library/Frameworks/R.framework/Resources/bin/build: line 10: 91104 Done                    echo 'tools:::.build_packages()'
        91105 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --slave --args ${args}
Error: Failed to install 'clustifyrdata' from GitHub:
  System command 'R' failed, exit status: 137, stdout + stderr:
E> * checking for file ‘/private/var/folders/fq/_zr6nbj12vlg13hz53xj2vgr0000gn/T/RtmpSyRqhZ/remotes163bb3b598210/rnabioco-clustifyrdata-8582364/DESCRIPTION’ ... OK
E> * preparing ‘clustifyrdata’:
E> * checking DESCRIPTION meta-information ... OK
E> * checking for LF line-endings in source and make files and shell scripts
E> * checking for empty or unneeded directories
E> * looking to see if a ‘data/datalist’ file should be added
E> /Library/Frameworks/R.framework/Resources/bin/build: line 10: 91104 Done                    echo 'tools:::.build_packages()'
E>      91105 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" --no-restore --slave --args ${args}
> 

   Error: processing vignette 'otherformats.Rmd' failed with diagnostics:
   `df` must be a data frame without row names in `column_to_rownames()`.
   --- failed re-building ‘otherformats.Rmd’

> SeuratIntegrate
An object of class Seurat 
30479 features across 191241 samples within 2 assays 
Active assay: integrated (2000 features, 2000 variable features)
 1 other assay present: RNA
 2 dimensional reductions calculated: pca, umap
> res <- clustify(
+     input = SeuratIntegrate,
+     ref_mat = ref_hema_microarray,
+     cluster_col = "integrated_snn_res.0.4"
+ )
found variable genes in SCT slot
Error in object_data.Seurat(s_object, "var.genes", n_genes) : 
  trying to get slot "var.features" from an object of a basic class ("NULL") with no slots

> tools::checkRdaFiles("data")
                                    size ASCII compress version
data/gtex_bulk_matrix.rda        4291717 FALSE    bzip2       2
data/immgen_ref.rda             17368211 FALSE    bzip2       2
data/mouse.rnaseq_ref.rda        3425344 FALSE    bzip2       2
data/pan_indrop_avg.rda          1285269 FALSE    bzip2       2
data/pan_indrop_markers.rda       250580 FALSE    bzip2       2
data/pan_indrop_matrix.rda      19337051 FALSE    bzip2       2
data/pan_indrop_meta.rda          152107 FALSE    bzip2       2
data/pan_indrop_vargenes.rda        9632 FALSE    bzip2       2
data/pan_smartseq2_avg.rda       1803778 FALSE    bzip2       2
data/pan_smartseq2_matrix.rda   31234423 FALSE    bzip2       2
data/pan_smartseq2_meta.rda        42874 FALSE    bzip2       2
data/pan_smartseq2_vargenes.rda    18535 FALSE    bzip2       2
data/pbmc4k_avg.rda              1025525 FALSE    bzip2       2
data/pbmc4k_markers.rda           146440 FALSE    bzip2       2
data/pbmc4k_markers_M3Drop.rda     11754 FALSE    bzip2       2
data/pbmc4k_matrix.rda           8269555 FALSE    bzip2       2
data/pbmc4k_meta.rda               98494 FALSE    bzip2       2
data/pbmc4k_vargenes.rda           10593 FALSE    bzip2       2
data/pbmc5_markers.rda            191771 FALSE    bzip2       2
data/pbmc5_matrix.rda           18104217 FALSE    bzip2       2
data/pbmc5_meta.rda               171490 FALSE    bzip2       2
data/pbmc_bulk_matrix.rda         591426 FALSE    bzip2       2
data/pbmc_pca.rda                   2279 FALSE     gzip       2
data/ref_tabula_muris_drop.rda  10525886 FALSE    bzip2       2
data/ref_tabula_muris_facs.rda  20130052 FALSE    bzip2       2
data/yan_ref.rda                  284913 FALSE    bzip2       2

Warning: namespace ‘Seurat’ is not available and has been replaced
by .GlobalEnv when processing object ‘s_small3’