Visual interface not starting with new R v.4.1.1

[SaraL-GH]

Hello, I have updated my R and RStudio, re-installed all the packages (I had saved the list) but now I am having issues while using psichomics() to open the web interface. I've got shiny and shinyBS installed, I am not sure if there are any other dependencies that for some reason were not re-installed in my new version of R. I'm copying the messages I get, it would be amazing to have some help:

library(psichomics) Loading required package: shiny Loading required package: shinyBS Registered S3 method overwritten by 'quantmod': method from as.zoo.data.frame zoo Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.18.5: start the visual interface by running psichomics() Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics

psichomics() This Font Awesome icon ('envelope-o') does not exist:

• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('thumb-tack') is deprecated in Font Awesome 5:
• please consider using 'thumbtack' or 'fas fa-thumbtack' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('thumb-tack') is deprecated in Font Awesome 5:
• please consider using 'thumbtack' or 'fas fa-thumbtack' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('thumb-tack') is deprecated in Font Awesome 5:
• please consider using 'thumbtack' or 'fas fa-thumbtack' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('thumb-tack') is deprecated in Font Awesome 5:
• please consider using 'thumbtack' or 'fas fa-thumbtack' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('sliders') is deprecated in Font Awesome 5:
• please consider using 'sliders-h' or 'fas fa-sliders-h' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('calendar-times-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('pencil') is deprecated in Font Awesome 5:
• please consider using 'pencil-alt' or 'fas fa-pencil-alt' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('pencil') is deprecated in Font Awesome 5:
• please consider using 'pencil-alt' or 'fas fa-pencil-alt' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('file-text') is deprecated in Font Awesome 5:
• please consider using 'file-alt' or 'fas fa-file-alt' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('envelope-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE Error in nav[[3]][[1]][[3]][[1]][[3]][[2]] : subscript out of bounds

Thanks in advance!

[nuno-agostinho]

Hey @SaraL-GH, the problem is related with using psichomics 1.18.5 (or lower) and shiny 1.7.0.

I already fixed this in psichomics 1.18.6. This version should be available in Bioconductor soon. If you want, you can already install the newest version from GitHub via R:

install.packages("remotes")
remotes::install_github("nuno-agostinho/psichomics@1.18.6")

Note that if you install psichomics via GitHub, you won't get notifications to update to newer versions of psichomics (but you can always install the Bioconductor version afterwards if you want).

If you have further questions, feel free to ask! Best regards :)

[SaraL-GH]

Hi @nuno-agostinho , that fixed it! Thank you so much! All the best :)