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joey711 / shiny-phyloseq

An interactive web application for demonstrating and using phyloseq.
http://joey711.github.io/shiny-phyloseq
GNU General Public License v3.0
60 stars 45 forks source link

Errors deploying on shinyapps.io #80

Closed abalter closed 5 years ago

abalter commented 6 years ago

Before I reinvent the wheel (not that there is anything wrong with that in some cases) I wanted to check if you have been able to deploy this app on shinyapps.io.

I followed the instructions to deploy the application, but ran into some errors:

> rsconnect::deployApp('shiny-phyloseq')
Preparing to deploy application...DONE
Uploading bundle for application: 402164...--- Please select a CRAN mirror for use in this session ---
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'Transform.utf8'
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'palette.utf8'
Error: Unable to retrieve package records for the following packages:
- 'GenomeInfoDbData'
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  Package 'GenomeInfoDbData' not available in repository or locally
2: In FUN(X[[i]], ...) :
  Failed to infer source for package 'd3Network'; using latest available version on CRAN instead
3: In FUN(X[[i]], ...) :
  Failed to infer source for package 'png'; using latest available version on CRAN instead
>

suggestions?

spholmes commented 6 years ago

I am not quite sure about whether all the Bioconductor packages are available on the shiny platforms. I have not tried to deploy from servers recently, did you try locally first?

On Fri, Aug 17, 2018 at 11:45 AM Ariel Balter notifications@github.com wrote:

Before I reinvent the wheel (not that there is anything wrong with that in some cases) I wanted to check if you have been able to deploy this app on shinyapps.io http://www.shinyapps.io.

I followed the instructions http://docs.rstudio.com/shinyapps.io/getting-started.html#deploying-a-sample-application to deploy the application, but ran into some errors:

rsconnect::deployApp('shiny-phyloseq') Preparing to deploy application...DONE Uploading bundle for application: 402164...--- Please select a CRAN mirror for use in this session --- [WARNING] This document format requires a nonempty element. Please specify either 'title' or 'pagetitle' in the metadata. Falling back to 'Transform.utf8' [WARNING] This document format requires a nonempty <title> element. Please specify either 'title' or 'pagetitle' in the metadata. Falling back to 'palette.utf8' Error: Unable to retrieve package records for the following packages:</p> <ul> <li>'GenomeInfoDbData' In addition: Warning messages: 1: In FUN(X[[i]], ...) : Package 'GenomeInfoDbData' not available in repository or locally 2: In FUN(X[[i]], ...) : Failed to infer source for package 'd3Network'; using latest available version on CRAN instead 3: In FUN(X[[i]], ...) : Failed to infer source for package 'png'; using latest available version on CRAN instead</li> </ul> </blockquote> <p>suggestions?</p> <p>— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <a href="https://github.com/joey711/shiny-phyloseq/issues/80">https://github.com/joey711/shiny-phyloseq/issues/80</a>, or mute the thread <a href="https://github.com/notifications/unsubscribe-auth/ABJcvdCMX6hkSkga8m9RWII84qTZPLSUks5uRw9LgaJpZM4WCB2F">https://github.com/notifications/unsubscribe-auth/ABJcvdCMX6hkSkga8m9RWII84qTZPLSUks5uRw9LgaJpZM4WCB2F</a> .</p> </blockquote> <p>-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 <a href="http://www-stat.stanford.edu/~susan/">http://www-stat.stanford.edu/~susan/</a></p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/yaccos"><img src="https://avatars.githubusercontent.com/u/22662263?v=4" />yaccos</a> commented <strong> 5 years ago</strong> </div> <div class="markdown-body"> <p>I have indeed deployed the app to <a href="shinyapps.io">shinyapps.io</a>. The Bioconductor packages are available there, yes. However, the way shinyapps installs packages is a bit tricky: It searches through the source code, looks for the usages of packages and then installs them. You cannot use <code>install.packages</code> nor <code>biocLite</code> (when required packages are installed, everything works fine even on shinyapps). In this case, shinyapps does not know that the libraries <code>shinythemes</code> and <code>networkD3</code> are required (I consider the app's practice of including packages in a loop to be bad), so I had to put something into the code to tell that. <a href="https://github.com/yaccos/shiny-phyloseq">My fork</a> should work.</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/joey711"><img src="https://avatars.githubusercontent.com/u/841437?v=4" />joey711</a> commented <strong> 5 years ago</strong> </div> <div class="markdown-body"> <p>thanks @yaccos </p> </div> </div> <div class="page-bar-simple"> </div> <div class="footer"> <ul class="body"> <li>© <script> document.write(new Date().getFullYear()) </script> Githubissues.</li> <li>Githubissues is a development platform for aggregating issues.</li> </ul> </div> <script src="https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.min.js"></script> <script src="/githubissues/assets/js.js"></script> <script src="/githubissues/assets/markdown.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/highlight.min.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/languages/go.min.js"></script> <script> hljs.highlightAll(); </script> </body> </html>