can't load ADaM dataset: "Warning: Error in file: cannot open the connection"

[ElijT]

Hello, I have just discovered tidyCDISC package and had fun playing with it.

I did a local instal and was able to play around with pilot data without any fuzz.

While loading datasets, I have one file that did not load.

The error on the console was: Warning in file(con, "rb") : cannot open file 'inst/app/www/red_x.png': No such file or directory Warning: Error in file: cannot open the connection

I tried to load the file in R, re-export it to make sure that the file itself was not corrupted but without any impact. Any ideas on the troubleshooting steps?

Bests,

NB: Below sessionInfo(output)

`R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS 13.0.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] haven_2.5.1 shiny_1.7.4 tidyCDISC_0.2.0 devtools_2.4.5 usethis_2.1.6

loaded via a namespace (and not attached): [1] fs_1.6.1 fontawesome_0.5.0 insight_0.19.0 RColorBrewer_1.1-3 httr_1.4.4 rprojroot_2.0.3 tippy_0.1.0 tools_4.2.0 profvis_0.3.7
[10] bslib_0.4.2 DT_0.27 utf8_1.2.3 R6_2.5.1 sjlabelled_1.2.0 lazyeval_0.2.2 colorspace_2.1-0 urlchecker_1.0.1 withr_2.5.0
[19] tidyselect_1.2.0 prettyunits_1.1.1 GGally_2.1.2 processx_3.8.0 curl_5.0.0 compiler_4.2.0 cli_3.6.0 gt_0.8.0 xml2_1.3.3
[28] shinyjs_2.1.0 desc_1.4.2 plotly_4.10.1 sass_0.4.5 scales_1.2.1 readr_2.1.4 callr_3.7.3 stringr_1.5.0 digest_0.6.31
[37] rmarkdown_2.20 pkgconfig_2.0.3 htmltools_0.5.4 sessioninfo_1.2.2 attempt_0.3.1 fastmap_1.1.0 htmlwidgets_1.6.1 rlang_1.0.6 rstudioapi_0.14
[46] jquerylib_0.1.4 generics_0.1.3 jsonlite_1.8.4 crosstalk_1.2.0 dplyr_1.1.0 config_0.3.1 magrittr_2.0.3 Matrix_1.5-3 Rcpp_1.0.10
[55] munsell_0.5.0 fansi_1.0.4 lifecycle_1.0.3 stringi_1.7.12 IDEAFilter_0.1.2 yaml_2.3.7 pkgbuild_1.4.0 plyr_1.8.8 shinyTime_1.0.3
[64] grid_4.2.0 promises_1.2.0.1 forcats_1.0.0 crayon_1.5.2 lattice_0.20-45 miniUI_0.1.1.1 splines_4.2.0 hms_1.1.2 knitr_1.42
[73] ps_1.7.2 pillar_1.8.1 pkgload_1.3.2 glue_1.6.2 cicerone_1.0.4 evaluate_0.20 golem_0.3.5 data.table_1.14.8 remotes_2.4.2
[82] tzdb_0.3.0 vctrs_0.5.2 httpuv_1.6.9 gtable_0.3.1 purrr_1.0.1 tidyr_1.3.0 reshape_0.8.9 assertthat_0.2.1 cachem_1.0.6
[91] ggplot2_3.4.1 xfun_0.37 mime_0.12 xtable_1.8-4 roxygen2_7.2.3 later_1.3.0 ggcorrplot_0.1.4 survival_3.5-3 viridisLite_0.4.1 [100] tibble_3.1.8 memoise_2.0.1 shinyWidgets_0.7.6 ellipsis_0.3.2 timevis_2.1.0 `

[ElijT]

After diving in closed issues, it might be a duplicate of Issues loading non-ADSL datasets #27. I have tried to install from CRAN and from devtools::install_github() and got similar results.

The following warning message might be a clue: 'Warning in file(con, "rb") : cannot open file 'inst/app/www/red_x.png': No such file or directory'

For the record, I looked, and the file red_x is present and permissions appears to be read for everyone, rw for me.

[AARON-CLARK]

Hi @ElijT, thanks for opening an issue and my apologies for not getting to it sooner.

So, the data compliance module is clearly finding something wrong with the data you uploaded. Please read the app's Upload Requirements or click the [❔] button on Data tab in the app to learn more.

You successfully identified a bug that arises when accessing that png file though. I was able to reproduce your error and I've submitted a small patch on GitHub. If you run the code below in a fresh R session, you should be able to re-run the app and that error should go away on upload, and thus revealing what specific upload requirement your data is violating.

remotes::install_github("Biogen-Inc/tidyCDISC", ref = "ac-166-access-png") # May Require Rtools
packageVersion("tidyCDISC") # should be v0.2.1
tidyCDISC::run_app()

Please let me know if that doesn't work for you. I'll close this issue when that branch get's merged into master. If there are any other questions or feature requests you have for the app, we'd love to hear more from you! Thanks again.

[ElijT]

Hi @AARON-CLARK , Thank you for the reply and help.

I did try to update the package and it dit not fully helped.

When running tidyCDISC::run_app(), I get the following error message

Listening on http://127.0.0.1:4786 The name provided ('chevron-down w3-tiny') does not correspond to a known icon Warning in structure(d <- filter_returns[[utils::tail(filters(), 1)]]$data(), : Calling 'structure(NULL, )' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), )' instead.

Pilot CDISC is able to load without issue (and table are working).

Now I tried to re-upload my ADSL file. There is no warning after upload by a message in the console:

Warning: Unknown or uninitialised column: PARAMCD. Warning: Unknown or uninitialised column: PARAMCD.

There might be an issue in my specific dataset that makes it thinks that it is not an ADSL dataset? The ADSL dataset still is available, but creating tables is impossible (can't drag values). I have just tried the dataset from scda package, and I still cant create tables

Thank you for looking into the issue, do let me know if there is anything you would like me to test!

[AARON-CLARK]

Hi @ElijT, glad to hear the "data compliance" issue went away! However, the issue you're observing now is unrelated and unexpected. I can reproduce your problem with consistency so we'll escalate it to a high priority and likely submit a hot patch to CRAN. Thank you for reporting it! I've created a new issue if you'd like to track it (#173).