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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
59 stars 45 forks source link

Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found #81

Closed gitIssues2018 closed 5 years ago

gitIssues2018 commented 6 years ago

Hello, I received the error "Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found." I noted this was an issue in 2017 as well. Please let me know the easiest way to fix this error.

spholmes commented 6 years ago

The automatic install is definitely out of date, sorry about that, we should revise it with the new BiocManager ( https://cran.r-project.org/web/packages/BiocManager/index.html). Probably the best is to install all the packages listed by hand and skip the automatic install, and install the packages that it says it needs by hand as needed. A good start is to install shiny and

phyloseq

shiny,shinythemes, ggplot2,data.table, grid, gridExtra, markdown , rmarkdown , png, RColorBrewer , scales

On Sat, Aug 18, 2018 at 7:51 AM gitIssues2018 notifications@github.com wrote:

Hello, I received the error "Error in biocLite(i, suppressUpdates = TRUE) : object 'i' not found." I noted this was an issue in 2017 as well. Please let me know the easiest way to fix this error.

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-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

yaccos commented 5 years ago

@spholmes: Good point, but that is not actually the bug. This is the same bug reported in #73. Unfortunately, this repository does not seem to be maintained anymore (right @joey711?). If you look for a fork where the bug is fixed, you can consider mine.

joey711 commented 5 years ago

Citation needed. This repo is supported. The bug was due to a breaking change in Bioconductor installation. The change was easy to migrate in the install script. It should now be working if you update to the latest commit on master branch. Please re-open if problem persists...