With v0.3.31 prepareTemplate can't find files for markdown

[sjmonkley]

Managed to install v 0.3.31 but it now failed at the prepareTemplate step

> prepareTemplate(package = "bcbioRNASeq")
Error in system.file("rmarkdown", "shared", package = package, mustWork = TRUE) : 
  no file found

Appears prepareTemplate can't find the files it need for Markdown in the bcbioRNAseq package

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

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

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

other attached packages:
 [1] bcbioRNASeq_0.3.31          basejump_0.12.2             DESeq2_1.26.0               SummarizedExperiment_1.16.1 DelayedArray_0.12.2         BiocParallel_1.20.1        
 [7] matrixStats_0.55.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.0         IRanges_2.20.2              S4Vectors_0.24.3           
[13] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1              ggridges_0.5.2                htmlTable_1.13.3              XVector_0.26.0                base64enc_0.1-3               rstudioapi_0.11              
  [7] ggrepel_0.8.1                 bit64_0.9-7                   fansi_0.4.1                   interactiveDisplayBase_1.24.0 AnnotationDbi_1.48.0          splines_3.6.1                
 [13] R.methodsS3_1.8.0             tximport_1.14.0               goalie_0.4.2                  geneplotter_1.64.0            knitr_1.28                    Formula_1.2-3                
 [19] Rsamtools_2.2.1               annotate_1.64.0               cluster_2.1.0                 dbplyr_1.4.2                  png_0.1-7                     R.oo_1.23.0                  
 [25] pheatmap_1.0.12               shiny_1.4.0                   BiocManager_1.30.10           compiler_3.6.1                httr_1.4.1                    backports_1.1.5              
 [31] assertthat_0.2.1              Matrix_1.2-18                 fastmap_1.0.1                 lazyeval_0.2.2                limma_3.42.2                  cli_2.0.1                    
 [37] acidbase_0.1.5                later_1.0.0                   acepack_1.4.1                 htmltools_0.4.0               prettyunits_1.1.1             tools_3.6.1                  
 [43] gtable_0.3.0                  glue_1.3.1                    GenomeInfoDbData_1.2.2        dplyr_0.8.4                   acidplots_0.2.23              rappdirs_0.3.1               
 [49] Rcpp_1.0.3                    vctrs_0.2.2                   Biostrings_2.54.0             rtracklayer_1.46.0            xfun_0.12                     stringr_1.4.0                
 [55] syntactic_0.3.7               mime_0.9                      lifecycle_0.1.0               ensembldb_2.10.2              XML_3.99-0.3                  edgeR_3.28.0                 
 [61] AnnotationHub_2.18.0          zlibbioc_1.32.0               scales_1.1.0                  ProtGenerics_1.18.0           hms_0.5.3                     promises_1.1.0               
 [67] AnnotationFilter_1.10.0       RColorBrewer_1.1-2            SingleCellExperiment_1.8.0    yaml_2.2.1                    curl_4.3                      memoise_1.1.0                
 [73] gridExtra_2.3                 UpSetR_1.4.0                  ggplot2_3.2.1                 biomaRt_2.42.0                rpart_4.1-15                  latticeExtra_0.6-29          
 [79] stringi_1.4.6                 RSQLite_2.2.0                 BiocVersion_3.10.1            genefilter_1.68.0             checkmate_2.0.0               GenomicFeatures_1.38.1       
 [85] rlang_0.4.4                   pkgconfig_2.0.3               bitops_1.0-6                  lattice_0.20-38               purrr_0.3.3                   GenomicAlignments_1.22.1     
 [91] htmlwidgets_1.5.1             cowplot_1.0.0                 bit_1.1-15.2                  tidyselect_1.0.0              plyr_1.8.5                    magrittr_1.5                 
 [97] R6_2.4.1                      acidgenerics_0.3.4            Hmisc_4.3-1                   DBI_1.1.0                     withr_2.1.2                   pillar_1.4.3                 
[103] foreign_0.8-75                survival_3.1-8                RCurl_1.98-1.1                nnet_7.3-12                   bcbioBase_0.6.13              pipette_0.4.1                
[109] tibble_2.1.3                  crayon_1.3.4                  BiocFileCache_1.10.2          jpeg_0.1-8.1                  progress_1.2.2                locfit_1.5-9.1               
[115] grid_3.6.1                    data.table_1.12.8             blob_1.2.1                    digest_0.6.24                 xtable_1.8-4                  httpuv_1.5.2                 
[121] R.utils_2.9.2                 openssl_1.4.1                 munsell_0.5.0                 sessioninfo_1.1.1             askpass_1.1  

[mjsteinbaugh]

Thanks I'll take a look. In the meantime, try running with just prepareTemplate(), which will use files from basejump instead. See here for files: https://github.com/acidgenomics/basejump/tree/master/inst/rmarkdown/shared

[mjsteinbaugh]

Ah OK I see the issue. Be sure to update your R Markdown code to match the latest templates here: https://github.com/hbc/bcbioRNASeq/tree/master/inst/rmarkdown/templates

[mjsteinbaugh]

prepareTemplate(package = "bcbioRNASeq") is now defunct in favor of simply prepareTemplate(). I'll work on improving this error message in the latest version of basejump. Thanks for the heads up.

[sjmonkley]

Thanks for the answer- I should have thought of this myself but was wanting to 'quickly' rerun an old template with new contrasts (and it was friday afternoon). Will check the new template and update accordingly