Minor issue in vignette

Simple, but it looks like the rendered version of the vignette, built during install is missing the following chunk that is required for the pipeline to work. The chunk options may be set to hide code?

Chunk:

## Find differentially expressed genes

__This is the step where we generate the input for CIPR's log fold change (logFC) comparison methods.__

{r, echo=F, results="hide"}
allmarkers <- FindAllMarkers(pbmc)

This could just be an issue with the local build so here is my session info:

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_Ireland.1252  LC_CTYPE=English_Ireland.1252    LC_MONETARY=English_Ireland.1252
[4] LC_NUMERIC=C                     LC_TIME=English_Ireland.1252    

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] knitr_1.37                  SeuratObject_4.0.4          Seurat_4.0.6               
 [4] CIPR_0.1.0                  cowplot_1.1.1               svglite_2.0.0              
 [7] ggforce_0.3.3               lattice_0.20-45             gridExtra_2.3              
[10] RColorBrewer_1.1-2          forcats_0.5.1               stringr_1.4.0              
[13] dplyr_1.0.6                 purrr_0.3.4                 readr_2.1.1                
[16] tidyr_1.1.4                 tibble_3.1.5                tidyverse_1.3.1            
[19] scater_1.18.6               ggplot2_3.3.5               SingleCellExperiment_1.12.0
[22] SummarizedExperiment_1.20.0 Biobase_2.50.0              GenomicRanges_1.42.0       
[25] GenomeInfoDb_1.26.7         IRanges_2.24.1              S4Vectors_0.28.1           
[28] BiocGenerics_0.36.1         MatrixGenerics_1.2.1        matrixStats_0.61.0         

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                reticulate_1.22           tidyselect_1.1.1          htmlwidgets_1.5.4        
  [5] BiocParallel_1.24.1       Rtsne_0.15                devtools_2.4.2            munsell_0.5.0            
  [9] codetools_0.2-18          ica_1.0-2                 future_1.23.0             miniUI_0.1.1.1           
 [13] withr_2.4.3               colorspace_2.0-2          highr_0.9                 rstudioapi_0.13          
 [17] ROCR_1.0-11               tensor_1.5                listenv_0.8.0             GenomeInfoDbData_1.2.4   
 [21] polyclip_1.10-0           farver_2.1.0              rprojroot_2.0.2           parallelly_1.30.0        
 [25] vctrs_0.3.8               generics_0.1.1            xfun_0.29                 R6_2.5.1                 
 [29] ggbeeswarm_0.6.0          rsvd_1.0.5                spatstat.utils_2.3-0      bitops_1.0-7             
 [33] cachem_1.0.4              DelayedArray_0.16.3       assertthat_0.2.1          promises_1.2.0.1         
 [37] scales_1.1.1              beeswarm_0.4.0            gtable_0.3.0              beachmat_2.6.4           
 [41] globals_0.14.0            goftest_1.2-3             processx_3.5.2            rlang_0.4.10             
 [45] systemfonts_1.0.3         splines_4.0.3             lazyeval_0.2.2            spatstat.geom_2.3-1      
 [49] broom_0.7.10              abind_1.4-5               reshape2_1.4.4            yaml_2.2.1               
 [53] modelr_0.1.8              backports_1.4.1           httpuv_1.6.4              tools_4.0.3              
 [57] usethis_2.1.3             spatstat.core_2.3-2       ellipsis_0.3.2            jquerylib_0.1.4          
 [61] sessioninfo_1.2.2         ggridges_0.5.3            Rcpp_1.0.7                plyr_1.8.6               
 [65] sparseMatrixStats_1.2.1   zlibbioc_1.36.0           RCurl_1.98-1.5            ps_1.6.0                 
 [69] prettyunits_1.1.1         rpart_4.1-15              deldir_1.0-6              pbapply_1.5-0            
 [73] viridis_0.6.2             zoo_1.8-9                 haven_2.4.3               ggrepel_0.9.1            
 [77] cluster_2.1.2             fs_1.5.0                  magrittr_2.0.1            scattermore_0.7          
 [81] data.table_1.14.2         lmtest_0.9-39             reprex_2.0.1              RANN_2.6.1               
 [85] fitdistrplus_1.1-6        pkgload_1.2.4             hms_1.1.1                 patchwork_1.1.1          
 [89] mime_0.12                 evaluate_0.14             xtable_1.8-4              readxl_1.3.1             
 [93] testthat_3.1.0            compiler_4.0.3            KernSmooth_2.23-20        crayon_1.4.2             
 [97] htmltools_0.5.2           mgcv_1.8-38               later_1.3.0               tzdb_0.2.0               
[101] lubridate_1.8.0           DBI_1.1.2                 tweenr_1.0.2              dbplyr_2.1.1             
[105] MASS_7.3-54               Matrix_1.4-0              cli_3.1.0                 igraph_1.2.10            
[109] pkgconfig_2.0.3           spatstat.sparse_2.1-0     plotly_4.10.0             scuttle_1.0.4            
[113] xml2_1.3.3                vipor_0.4.5               bslib_0.3.1               XVector_0.30.0           
[117] rvest_1.0.2               callr_3.7.0               digest_0.6.27             sctransform_0.3.2        
[121] RcppAnnoy_0.0.19          spatstat.data_2.1-2       rmarkdown_2.11            cellranger_1.1.0         
[125] leiden_0.3.9              uwot_0.1.11               DelayedMatrixStats_1.12.3 curl_4.3.1               
[129] shiny_1.7.1               nlme_3.1-153              lifecycle_1.0.1           jsonlite_1.7.2           
[133] BiocNeighbors_1.8.2       limma_3.46.0              desc_1.4.0                viridisLite_0.4.0        
[137] fansi_0.5.0               pillar_1.6.4              fastmap_1.1.0             httr_1.4.2               
[141] pkgbuild_1.3.1            survival_3.2-13           glue_1.4.2                remotes_2.4.2            
[145] png_0.1-7                 stringi_1.7.6             sass_0.4.0                BiocSingular_1.6.0       
[149] memoise_2.0.1             irlba_2.3.5               future.apply_1.8.1

atakanekiz / CIPR-Package

Minor issue in vignette #5