GUI crashes when trying to load .mzid file

Hi @thomasp85,

I am trying to visualise a .mzid file I have previously generated using your MSGFplus package. Nice work btw! The resulting file can be parsed using the mzID package:

> results <- mzID("/Users/tobiasko/Downloads/20181113_010_autoQC01.mzid")
reading 20181113_010_autoQC01.mzid... DONE!
> results
An mzID object

Software used:   MS-GF+ (version: Beta (v10072))

Rawfile:         /Users/tobiasko/Downloads/20181113_010_autoQC01.mzML

Database:        /Users/tobiasko/Downloads/uniprot-proteome_UP000005640_irtfusion.fasta

Number of scans: 11780
Number of PSM's: 14237

But when I try to load it using the MSGFgui I get the following output on the R console:

> MSGFgui()

Listening on http://127.0.0.1:6938
reading 20181113_010_autoQC01.mzid... DONE!
Warning: Error in scans: could not find function "scans"
  60: <Anonymous>
  45: <observer>
   2: runApp
   1: MSGFgui

Is scans() a function of your package? Or do I need to load dependency I am not aware of?

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shiny_1.5.0    MSGFgui_1.22.0 xlsx_0.6.5     mzR_2.22.0     Rcpp_1.0.5    
[6] mzID_1.26.0   

loaded via a namespace (and not attached):
 [1] nlme_3.1-149          ProtGenerics_1.20.0   bitops_1.0-6          doParallel_1.0.16    
 [5] tools_4.0.2           backports_1.1.10      R6_2.4.1              KernSmooth_2.23-17   
 [9] BiocGenerics_0.34.0   colorspace_1.4-1      withr_2.3.0           tidyselect_1.1.0     
[13] compiler_4.0.2        preprocessCore_1.50.0 Biobase_2.48.0        caTools_1.18.0       
[17] scales_1.1.1          readr_1.3.1           stringr_1.4.0         digest_0.6.25        
[21] minqa_1.2.4           rmarkdown_2.6         pkgconfig_2.0.3       htmltools_0.5.1.1    
[25] lme4_1.1-23           fastmap_1.0.1         limma_3.44.3          rlang_0.4.9          
[29] rstudioapi_0.11       generics_0.0.2        jsonlite_1.7.1        gtools_3.8.2         
[33] dplyr_1.0.2           magrittr_1.5          Matrix_1.2-18         munsell_0.5.0        
[37] lifecycle_0.2.0       stringi_1.5.3         yaml_2.2.1            MSGFplus_1.24.0      
[41] MASS_7.3-53           RJSONIO_1.3-1.4       gplots_3.1.0          plyr_1.8.6           
[45] grid_4.0.2            shinyFiles_0.6.2      parallel_4.0.2        promises_1.1.1       
[49] ggrepel_0.8.2         crayon_1.3.4          doSNOW_1.0.18         MSstats_3.20.3       
[53] lattice_0.20-41       splines_4.0.2         xlsxjars_0.6.1        hms_0.5.3            
[57] knitr_1.30            pillar_1.4.6          boot_1.3-25           reshape2_1.4.4       
[61] codetools_0.2-16      marray_1.66.0         XML_3.99-0.5          glue_1.4.2           
[65] evaluate_0.14         data.table_1.13.0     vctrs_0.3.4           nloptr_1.2.2.2       
[69] httpuv_1.5.4          foreach_1.5.0         gtable_0.3.0          purrr_0.3.4          
[73] tidyr_1.1.2           ggplot2_3.3.2         xfun_0.19             mime_0.9             
[77] xtable_1.8-4          broom_0.7.1           later_1.1.0.1         ncdf4_1.17           
[81] survival_3.2-7        minpack.lm_1.2-1      tibble_3.0.3          snow_0.4-3           
[85] rJava_0.9-13          iterators_1.0.12      statmod_1.4.34        ellipsis_0.3.1       
>

thomasp85 / MSGFgui

GUI crashes when trying to load .mzid file #36