shinythemes issue

[sokoloko]

Hello @joey711 @spholmes and thank you for phyloseq.

On previous R versions shiny worked, but since I upgraded to R 3.3.1 it doesn't. shinythemes seems to be missing. Is there a solution, please?

Best, Sergios

> shiny::runGitHub("shiny-phyloseq","joey711")
Downloading https://github.com/joey711/shiny-phyloseq/archive/master.tar.gz
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
The following package is missing.
shinythemes
Installation will be attempted...
Error in match(x, table, nomatch = 0L) : object 'i' not found

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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_0.14.1         BiocInstaller_1.24.0 devtools_1.12.0     

loaded via a namespace (and not attached):
 [1] httr_1.2.1      R6_2.2.0        htmltools_0.3.5 tools_3.3.1    
 [5] withr_1.0.2     curl_2.1        Rcpp_0.12.7     memoise_1.0.0  
 [9] git2r_0.15.0    jsonlite_1.1    digest_0.6.10   xtable_1.8-2   
[13] httpuv_1.3.3    mime_0.5  

[spholmes]

For some reason, the current version of Shiny-phyloseq doesn't find the packages shinythemes, rmarkdown and network3D Installing these by hand: install.packages("shinythemes") install.packages("networkD3") install.packages("rmarkdown") then rerunning

shiny::runGitHub("shiny-phyloseq","joey711")

[joey711]

Thanks! I'll take a look and update it

[spholmes]

I'm being picky because I am preparing to show this at NIPS tomorrow in front of 6,000 people, I think I am going to minimovie it rather than crash interactively for such a big crowd...

On Wed, Dec 7, 2016 at 6:54 PM, Paul J. McMurdie [email protected] wrote:

Thanks! I'll take a look and update it

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/68#issuecomment-265520438, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvWrYkCG0NUSQDJUsM853yQI78llBks5rFvLSgaJpZM4Kdkoq .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[joey711]

good idea (minimovie). Not worth the risk.

Btw I have some updates brewing. The new "shiny modules" are a great new addition for complex apps like shiny-phyloseq.

[spholmes]

Well, I wasn't able to make the mini-movie, this old bug with the provenance tracking cam back to haunt me:

Error in which: argument to 'which' is not logical

appears in the white screen when doing the provenance tracking or display code option...

doesn't matter, I'll point to Github and hope we have a fix soon.

On Wed, Dec 7, 2016 at 12:09 PM, Paul J. McMurdie [email protected] wrote:

good idea (minimovie). Not worth the risk.

Btw I have some updates brewing. The new "shiny modules" are a great new addition for complex apps like shiny-phyloseq.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/68#issuecomment-265559319, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvZWq6ADet-WIRcK_FFnuJVr-tSE0ks5rFxKRgaJpZM4Kdkoq .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/