Error in opening file on shiny page

[hpbenton]

When selecting the 'Select mzML files' or 'Select sample-group file' we get the error --

Warning: Error in structure: [tcl] invalid command name "tk_getOpenFile".

and the application closes but the connection is staying open.

sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] shiny_1.6.0 mzRAPP_1.1.4 xcms_3.14.0 MSnbase_2.18.0
[5] ProtGenerics_1.24.0 S4Vectors_0.30.0 mzR_2.26.1 Biobase_2.52.0
[9] BiocGenerics_0.38.0 BiocParallel_1.26.1 geoRge_1.0 Rcpp_1.0.6

loaded via a namespace (and not attached): [1] retistruct_0.6.3 colorspace_2.0-2 ellipsis_0.3.2
[4] XVector_0.32.0 GenomicRanges_1.44.0 clue_0.3-59
[7] affyio_1.62.0 fansi_0.5.0 codetools_0.2-18
[10] ncdf4_1.17 doParallel_1.0.16 cachem_1.0.5
[13] impute_1.66.0 robustbase_0.93-8 knitr_1.33
[16] jsonlite_1.7.2 cluster_2.1.2 vsn_3.60.0
[19] shinydashboard_0.7.1 BiocManager_1.30.16 compiler_4.1.0
[22] httr_1.4.2 assertthat_0.2.1 Matrix_1.3-4
[25] fastmap_1.1.0 lazyeval_0.2.2 limma_3.48.1
[28] later_1.2.0 htmltools_0.5.1.1 tools_4.1.0
[31] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.6
[34] affy_1.70.0 RANN_2.6.1 dplyr_1.0.7
[37] tinytex_0.32 MALDIquant_1.19.3 jquerylib_0.1.4
[40] vctrs_0.3.8 preprocessCore_1.54.0 iterators_1.0.13
[43] crosstalk_1.1.1 ttutils_1.0-1 xfun_0.24
[46] enviPat_2.4 mime_0.11 miniUI_0.1.1.1
[49] lifecycle_1.0.0 shinycssloaders_1.0.0 XML_3.99-0.6
[52] DEoptimR_1.0-9 zlibbioc_1.38.0 MASS_7.3-54
[55] scales_1.1.1 pcaMethods_1.84.0 promises_1.2.0.1
[58] MatrixGenerics_1.4.0 SummarizedExperiment_1.22.0 MassSpecWavelet_1.58.0
[61] RColorBrewer_1.1-2 yaml_2.2.1 ggplot2_3.3.5
[64] sass_0.4.0 foreach_1.5.1 manipulateWidget_0.11.0
[67] geometry_0.4.5 GenomeInfoDb_1.28.1 rlang_0.4.11
[70] pkgconfig_2.0.3 matrixStats_0.59.0 bitops_1.0-7
[73] rgl_0.106.8 mzID_1.30.0 evaluate_0.14
[76] lattice_0.20-44 purrr_0.3.4 htmlwidgets_1.5.3
[79] tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.1
[82] R6_2.5.0 IRanges_2.26.0 generics_0.1.0
[85] DelayedArray_0.18.0 DBI_1.1.1 pillar_1.6.1
[88] MsCoreUtils_1.4.0 abind_1.4-5 RCurl_1.98-1.3
[91] tibble_3.1.2 crayon_1.4.1 shinyWidgets_0.6.0
[94] utf8_1.2.1 plotly_4.9.4.1 rmarkdown_2.9
[97] grid_4.1.0 data.table_1.14.0 digest_0.6.27
[100] xtable_1.8-4 tidyr_1.1.3 httpuv_1.6.1
[103] munsell_0.5.0 viridisLite_0.4.0 bslib_0.2.5.1
[106] tcltk_4.1.0 magic_1.5-9 shinyjs_2.0.0

[YasinEl]

Hello and thank you for reporting the bug! It seems that this is an older rstudio issue when using tcltk::tk_choose.files() with Ubuntu (see https://github.com/rstudio/rstudio/issues/5545). I will try to come up with an alternative solution for this asap. In the meantime, I hope mzRAPP is still working when running without the GUI?

[YasinEl]

I have now implemented another package for file-selection if an OS.type other than Windows is used and submitted this newer version of mzRAPP to a side-branch of the GitHub repository. You can install it using remotes::install_github("https://github.com/YasinEl/mzRAPP",ref = "shinyFiles_if_not_windows").

Can you please check if this solves the problem for you?

[stolltho]

Hi Yasin, I have a similar problem on Windows w/ latest rstudio. Upon selecting tab 'Select mzML files' or 'Select sample-group file' etc. nothing happens and rstudio freezes. cheers, Thomas

[YasinEl]

Hello,

sorry to hear that. That sounds very strange! Have you checked if the file-selection window appeared just behind the R-Studio window? Unfortunately, that happens sometimes. In case that was not the problem I have now removed the tcltk-package completely for this branch (also for windows) can you please try to reinstall mzRAPP using remotes::install_github("https://github.com/YasinEl/mzRAPP",ref = "shinyFiles_if_not_windows") and check if that solves the problem?

Yasin

[YasinEl]

I have now merged the adapted version into the main branch. It should work for Ubuntu 20.04 as well as for Windows 10. Therefore, you can install it again via devtools::install_github("YasinEl/mzRAPP", dependencies = TRUE, build_vignettes = TRUE)

[stolltho]

I works now. Thanks

[hpbenton]

@YasinEl - Can also confirm fixed. I'm on Rstudio server 1.4.1106 Thanks :)