vignette missing

[rrohwer]

When I follow your readme directions vignette("intro-diversity-estimation") nothing opens up. I looked inside the vignette folder and it looks like the .rmd files are there but I don't see any rendered html version.

Here's what I ran (R version 4):

install.packages("BiocManager")
BiocManager::install("phyloseq")

install.packages("devtools")
devtools::install_github("adw96/breakaway")

library(breakaway)
vignette("intro-diversity-estimation")

and message:

Warning message:
vignette ‘intro-diversity-estimation’ not found 

I also tried:

vignette("breakaway")

Thanks!

[adw96]

Hi @rrohwer ! Thanks for letting us know. I tried to reproduce your error and did with

devtools::install_github(repo="adw96/breakaway", build_vignettes = TRUE, force=TRUE)

When I ran this, I was given the option for what packages to update, and chose "None", which gave me the same error that you received. When I reran this command and chose "All," the error disappeared. Going through the log files I think that our dependence on foreachwas causing problems and needed to be updated.

If you try this again with the "update all" option, could you please run

devtools::install_github(repo="adw96/breakaway", build_vignettes = TRUE, force=TRUE)
vignette("intro-diversity-estimation")

and let me know if this resolves your error?

[rrohwer]

Hi Amy, I am still getting an error. On my first try the error included messages about not having phyloseq and tidyverse, so I re-installed/updated these other packages:

install.packages("BiocManager")
BiocManager::install("phyloseq")
install.packages("devtools")
install.packages("tidyverse")

Next I tried your github installation again, but it ended with an error. It also included the same phyloseq error, (although there were no errors when I re-installed it). However the main error is about the vignette names not matching. Here is the full message it printed in the console:

> devtools::install_github(repo="adw96/breakaway", build_vignettes = TRUE, force=TRUE)
Downloading GitHub repo adw96/breakaway@master
Skipping 1 packages not available: phyloseq
✓  checking for file ‘/private/var/folders/mc/k9h2668x21vd_3ppxrkb5z7h0000gn/T/Rtmpz0j2br/remotes2f8b3cc6b5c0/adw96-breakaway-6da0cac/DESCRIPTION’ (533ms)
─  preparing ‘breakaway’:
✓  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
E  creating vignettes (1m 23.7s)
   --- re-building ‘breakaway.Rmd’ using rmarkdown
   Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "getting-started", and the latter is "Getting started with breakaway". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
   --- finished re-building ‘breakaway.Rmd’

   --- re-building ‘diversity-hypothesis-testing.Rmd’ using rmarkdown
   Quitting from lines 36-40 (diversity-hypothesis-testing.Rmd) 
   Error: processing vignette 'diversity-hypothesis-testing.Rmd' failed with diagnostics:
   there is no package called 'corncob'
   --- failed re-building ‘diversity-hypothesis-testing.Rmd’

   --- re-building ‘extended-tutorial.Rmd’ using rmarkdown
   Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "extended", and the latter is "Getting into the weeds". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
   --- finished re-building ‘extended-tutorial.Rmd’

   --- re-building ‘intro-diversity-estimation.Rmd’ using rmarkdown
   Quitting from lines 58-60 (intro-diversity-estimation.Rmd) 
   Error: processing vignette 'intro-diversity-estimation.Rmd' failed with diagnostics:
   there is no package called 'openxlsx'
   --- failed re-building ‘intro-diversity-estimation.Rmd’

   --- re-building ‘sample-size-calculations.Rmd’ using rmarkdown
   Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "sample-size-calculations", and the latter is "Sample size calculations for alpha diversity". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
   --- finished re-building ‘sample-size-calculations.Rmd’

   SUMMARY: processing the following files failed:
     ‘diversity-hypothesis-testing.Rmd’ ‘intro-diversity-estimation.Rmd’

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'breakaway' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> 
E> --- re-building ‘sample-size-calculations.Rmd’ using rmarkdown
E> Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "sample-size-calculations", and the latter is "Sample size calculations for alpha diversity". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
E> --- finished re-building ‘sample-size-calculations.Rmd’
E> 
E> SUMMARY: processing the following files failed:
E>   ‘diversity-hypothesis-testing.Rmd’ ‘intro-diversity-estimation.Rmd’
E> 
E> Error: Vignette re-building failed.
E> Execution halted

If this helps I am using R version 4.0.0 (2020-04-24) -- "Arbor Day" on a macOS Mojave 10.14.6.

Thanks! Robin

[adw96]

Hey @bryandmartin could you please help @rrohwer out on this one? Thanks!

[bryandmartin]

Hi @rrohwer !

We might need to do this iteratively. Let's try to remove as many of these issues at a time as we can and let me know what prints out.

First will you try the following

remotes::install_github("bryandmartin/corncob") install.packages("openxlsx")

After you get those both successfully installed, try installing breakaway again and let me know how it goes!

[rrohwer]

Hi @bryandmartin ,
This worked!

remotes::install_github("bryandmartin/corncob")
install.packages("openxlsx")
devtools::install_github(repo="adw96/breakaway", build_vignettes = TRUE, force=TRUE)
vignette("intro-diversity-estimation")

The vignette install portion took about 3 minutes creating vignettes (2m 51.1s), and the vignette opened as expected =)

Thanks so much for your help with the install and viewing the vignette. I stuck with it because I found your paper really interesting and I'm excited about trying out the package! But I'd suggest that others might find a link to a web-hosted version of the vignette useful- to peruse without the activation energy barrier of package installation.

Thanks again!
Robin

[bryandmartin]

Glad that worked Robin, I'll close the issue now. And you make a very reasonable point. @adw96 perhaps we could make a tab on the Diversity Lab page website to hold static PDFs that we could point to within the READMEs?

[afvrbanac]

Hello, I essentially had similar problems installing the vignettes, but couldn't resolve them. I wanted to second Robin's suggestion and say would be great if they were just hosted online for easy viewing in addition/instead. I'm not an R user so that would be the preferable way to view them. Thanks!

[adw96]

@bryandmartin Why wouldn't we host these PDFs under breakaway/vignettes? Why the lab website?

[adw96]

I'm reopening so I don't lose track of the issue for static PDFs

[svteichman]

I'm closing this because we've added static html files to the vignettes. I chose html files over pdfs because the vignettes currently knit to html and this seemed consistent. See pull request #129 for updates.