Peter Carbonetto

After some trial and error, it seems that misopy only works with samtools

Progress bar mimicking "progress" package

2

Thank you for providing this useful package. We have been using it to develop a new package (see [here](https://github.com/stephenslab/fastTopics)) and so far it is working very well. I have a...

Print more information about error when running wflow_git_push()

5

When I run `git push` in the shell I see this: ``` $ git push -u origin master Username for 'https://github.com': pcarbo Password for 'https://[email protected]': remote: Support for password authentication...

wflow_git_push with personal access token

3

@jdblischak @stephens999 I was able to successfully complete [all the steps in the tutorial](https://workflowr.github.io/workflowr/articles/wflow-01-getting-started.html) after creating a [personal access token (PAT)](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token): ```r library(workflowr) wflow_start() wflow_start("myproject2") wflow_build() wflow_publish(c("analysis/index.Rmd", "analysis/about.Rmd", "analysis/license.Rmd"), "Publish...

New "branch" argument for wflow_start()

1

@jdblischak @stephens999 Very recently, [git2r added a "branch" argument to init](https://cran.r-project.org/web/packages/git2r/news/news.html): ``` init(path = ".", bare = FALSE, branch = NULL) branch: Use the specified name for the initial branch...

Default setting for directory in wflow_start?

4

I'm wondering if it would make sense to set the default for `directory` in `wflow_start` to `getwd()`, or something like that.

Workflowr encourage use of relative file paths; however, this is not always possible, or not always the best idea. A workflowr user asked recently about how best to refer to...

It could be useful in some cases to (accurately) compute very small LFSRs (e.g. < 1e-16) --- if you want to compare with very small *p*-values, for example. I'm not...

Currently, `devtools::test()` returns `Error in x[[method]](...) : attempt to apply non-function`. There needs to be a `context` in every file. And we need to check for references to any non-exported...

KWDual outputs a negative mixture weight

7

Here is the example that produces a negative mixture weight with `optmethod = mixIP` only: ``` library(ashr) betahat