Error with html report creation

[jmvera255]

When I run flow_auto_qc with html_report set to a character string I get the following error Error in if (options$engine != "R") { : argument is of length zero

fcs_flowAI <- flow_auto_qc(fcs, 
                           folder_results = FALSE, 
                           fcs_QC = FALSE,
                           html_report = "test_flowAI", 
                           mini_report = FALSE)
Error in if (options$engine != "R") { : argument is of length zero

I think the issue occurs with knitting of the autoQC_report.Rmd template but I have yet to see where exactly the issue is.

R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.4.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] ComplexHeatmap_2.6.2 UpSetR_1.4.0         mixOmics_6.14.1      ggplot2_3.3.5        lattice_0.20-45     
 [6] MASS_7.3-55          flowCut_1.0.0        flowClean_1.28.0     flowAI_1.20.1        flowCore_2.2.0      
[11] dplyr_1.0.7         

loaded via a namespace (and not attached):
  [1] circlize_0.4.15      changepoint_2.2.4    spam_2.9-1           igraph_1.2.11        plyr_1.8.7          
  [6] sp_1.5-0             flowDensity_1.24.0   splines_4.0.5        RApiSerialize_0.1.2  BiocParallel_1.24.1 
 [11] RPMG_2.2-3           sva_3.38.0           digest_0.6.29        htmltools_0.5.5      viridis_0.6.2       
 [16] fansi_1.0.3          magrittr_2.0.3       memoise_2.0.1        Rwave_2.6-5          cluster_2.1.3       
 [21] sfsmisc_1.1-15       aws.signature_0.6.0  openxlsx_4.2.5.1     limma_3.46.0         annotate_1.68.0     
 [26] RcppParallel_5.1.5   matrixStats_0.61.0   rARPACK_0.11-0       flowWorkspace_4.2.0  cytolib_2.2.1       
 [31] jpeg_0.1-9           colorspace_2.0-3     ggrepel_0.9.1        blob_1.2.3           xfun_0.34           
 [36] jsonlite_1.7.3       crayon_1.5.2         hexbin_1.28.2        graph_1.68.0         genefilter_1.72.1   
 [41] stringfish_0.15.5    survival_3.3-1       zoo_1.8-11           glue_1.6.2           pals_1.7            
 [46] gtable_0.3.1         zlibbioc_1.36.0      GetoptLong_1.0.5     car_3.1-1            IDPmisc_1.1.20      
 [51] Rgraphviz_2.34.0     shape_1.4.6          BiocGenerics_0.36.1  maps_3.4.0           abind_1.4-5         
 [56] scales_1.1.1         DBI_1.1.3            edgeR_3.32.1         Rcpp_1.0.8           viridisLite_0.4.1   
 [61] xtable_1.8-4         clue_0.3-62          mapproj_1.2.8        bit_4.0.4            proxy_0.4-27        
 [66] RSEIS_4.1-4          dotCall64_1.0-2      stats4_4.0.5         httr_1.4.4           gplots_3.1.3        
 [71] RColorBrewer_1.1-3   ellipsis_0.3.2       pkgconfig_2.0.3      XML_3.99-0.11        sass_0.4.2          
 [76] GEOmap_2.5-0         flowViz_1.54.0       deldir_1.0-6         locfit_1.5-9.4       utf8_1.2.2          
 [81] tidyselect_1.1.1     rlang_1.0.6          reshape2_1.4.4       AnnotationDbi_1.52.0 munsell_0.5.0       
 [86] tools_4.0.5          cachem_1.0.6         cli_3.4.1            generics_0.1.3       RSQLite_2.2.18      
 [91] splancs_2.01-43      aws.s3_0.3.21        evaluate_0.17        stringr_1.4.1        fastmap_1.1.0       
 [96] yaml_2.3.5           knitr_1.40           bit64_4.0.5          zip_2.2.2            caTools_1.18.2      
[101] purrr_0.3.4          nlme_3.1-157         xml2_1.3.3           compiler_4.0.5       rstudioapi_0.14     
[106] curl_4.3.3           png_0.1-7            e1071_1.7-12         tibble_3.1.6         bslib_0.4.0         
[111] stringi_1.7.6        RSpectra_0.16-1      fields_14.1          rgeos_0.5-9          Matrix_1.5-3        
[116] vctrs_0.3.8          pillar_1.7.0         lifecycle_1.0.3      BiocManager_1.30.19  GlobalOptions_0.1.2 
[121] jquerylib_0.1.4      corpcor_1.6.10       data.table_1.14.4    bitops_1.0-7         R6_2.5.1            
[126] latticeExtra_0.6-30  qs_0.25.3            KernSmooth_2.23-20   gridExtra_2.3        RProtoBufLib_2.2.0  
[131] RFOC_3.4-6           IRanges_2.24.1       dichromat_2.0-0.1    gtools_3.9.3         assertthat_0.2.1    
[136] MBA_0.1-0            rjson_0.2.21         withr_2.5.0          S4Vectors_0.28.1     mgcv_1.8-40         
[141] parallel_4.0.5       ncdfFlow_2.36.0      tidyr_1.2.0          class_7.3-20         rmarkdown_2.17      
[146] carData_3.0-5        Cairo_1.6-0          Biobase_2.50.0       base64enc_0.1-3      ellipse_0.4.3       
[151] interp_1.1-3

[jmvera255]

this issue does not occur with the devel version.

[giannimonaco]

Great!

On Thu, Jun 29, 2023 at 9:12 PM Jessica Vera, Ph.D. < @.***> wrote:

this issue does not occur with the devel version.

— Reply to this email directly, view it on GitHub https://github.com/giannimonaco/flowAI/issues/18#issuecomment-1613665613, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2UTEBYM64XGLHDRWBMKBTXNXHTPANCNFSM6AAAAAAZYU7XHA . You are receiving this because you are subscribed to this thread.Message ID: @.***>