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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

Update for R 3.6 #84

Closed mspencercu closed 5 years ago

mspencercu commented 5 years ago

Can this be updated for R version 3.6? It won't let it be run without pointing to BiocManager.

spholmes commented 5 years ago

Hi: I have created a pull request to try and debug this by replacing bioclite with BiocManager::install. Thanks Susan

On Wed, Jul 17, 2019 at 7:15 AM mspencercu notifications@github.com wrote:

Can this be updated for R version 3.6? It won't let it be run without pointing to BiocManager.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/84?email_source=notifications&email_token=AAJFZPPKYKAJEIIPLTZS2B3P74SRLA5CNFSM4IEQ3VGKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G7YBT3Q, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJFZPKFSCTRVVEOO4Y6PELP74SRLANCNFSM4IEQ3VGA .

-- 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/

spholmes commented 5 years ago

The change you need to make is to make sure that BiocManager is installed with: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

and then replace the bioclite function install command with

if(missingPackage){ BiocManager::install(i) }

I did this by downloading my own copy of the gitub repo and manually changing the file install.R and then running the app from RSTudio

I hope this helps, Susan

On Wed, Jul 17, 2019 at 10:44 AM Susan Holmes sp.holmes@gmail.com wrote:

Hi: I have created a pull request to try and debug this by replacing bioclite with BiocManager::install. Thanks Susan

On Wed, Jul 17, 2019 at 7:15 AM mspencercu notifications@github.com wrote:

Can this be updated for R version 3.6? It won't let it be run without pointing to BiocManager.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/84?email_source=notifications&email_token=AAJFZPPKYKAJEIIPLTZS2B3P74SRLA5CNFSM4IEQ3VGKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G7YBT3Q, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJFZPKFSCTRVVEOO4Y6PELP74SRLANCNFSM4IEQ3VGA .

-- 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/

-- 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/

mspencercu commented 5 years ago

Thank you for helping Susan. I tried running it from devtools::source_url("https://raw.githubusercontent.com/spholmes/shiny-phyloseq/patch-1/install.R") but I get error, Error: object 'i' not found

Is there a way I should be installing it from github or do I have to copy my own repo?

spholmes commented 5 years ago

What I ended up doing was making my own copy by doing a fit clone of the http linked repo and doing the two edits that involved bioclite in the install.r file.

On Wed, Jul 17, 2019, 11:16 mspencercu notifications@github.com wrote:

Thank you for helping Susan. I tried running it from devtools::source_url(" https://raw.githubusercontent.com/spholmes/shiny-phyloseq/patch-1/install.R ") but I get error, Error: object 'i' not found

Is there a way I should be installing it from github or do I have to copy my own repo?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joey711/shiny-phyloseq/issues/84?email_source=notifications&email_token=AAJFZPOTWFTFIFG3KLHVC73P75OXDA5CNFSM4IEQ3VGKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GELRQ#issuecomment-512509382, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJFZPKIY5SGDJVWLBU25F3P75OXDANCNFSM4IEQ3VGA .

joey711 commented 5 years ago

This should be fixed in the update just-merged. Please re-open if the problem persists...

mspencercu commented 5 years ago

Error: object 'i' not found 16. stopifnot(is.character(pkgs), !anyNA(pkgs), .install_validate_dots(...), length(site_repository) <= 1L, is.character(site_repository), !any(is.na(site_repository)), is.logical(update), length(update) == 1L, !is.na(update), is.logical(ask), length(ask) == 1L, ... 15. BiocManager::install(i, update = FALSE) at install.R#20 14. (function (pkg, version = NULL, verbose = TRUE) { availpacks = .packages(all.available = TRUE) require("BiocManager") ... 13. mapply(install_missing_packages, pkg = names(deppkgs), version = deppkgs, MoreArgs = list(verbose = TRUE), SIMPLIFY = FALSE, USE.NAMES = TRUE) at install.R#67 12. eval(ei, envir) 11. eval(ei, envir) 10. withVisible(eval(ei, envir)) 9. source("install.R", local = TRUE) 8. ..stacktraceon..({ source("install.R", local = TRUE) source("core/default-parameters.R", local = TRUE) simpletime = function() { ... 7. eval(exprs, envir) 6. eval(exprs, envir) 5. sourceUTF8(file.path.ci(appDir, "global.R")) 4. appParts$onStart() 3. runApp(appdir, ...) 2. runUrl(url, subdir = subdir, destdir = destdir, ...) 1. shiny::runGitHub("shiny-phyloseq", "joey711")

mspencercu commented 5 years ago

This is the traceback for the error I get when trying to run it now.